diff --git a/Code/Mantid/Build/CMake/LinuxSetup.cmake b/Code/Mantid/Build/CMake/LinuxSetup.cmake
index 0a4fd2fb0a28d1bae9102182d034f727a0672c75..e9570ee1e02d693220a75a17f6a6cd0c6a24d317 100644
--- a/Code/Mantid/Build/CMake/LinuxSetup.cmake
+++ b/Code/Mantid/Build/CMake/LinuxSetup.cmake
@@ -47,21 +47,21 @@ set ( CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_PREFIX}/${LIB_DIR};${CMAKE_INSTALL_PRE
 
 file ( WRITE ${CMAKE_CURRENT_BINARY_DIR}/mantid.sh  "#!/bin/sh\n"
                                                     "MANTIDPATH=${CMAKE_INSTALL_PREFIX}/${BIN_DIR}\n"
-                                                    "PV_PLUGIN_PATH=${CMAKE_INSTALL_PREFIX}/${PVPLUGINS_DIR}\n"
+                                                    "PV_PLUGIN_PATH=${CMAKE_INSTALL_PREFIX}/${PVPLUGINS_DIR}/${PVPLUGINS_DIR}\n"
 #                                                    "scriptpath=\"$(cd \"\${0%/*}\" 2> /dev/null;echo \"$PWD\"/\"\${0##*/}\")\"\n"
 #                                                    "scriptpath=`readlink -f $scriptpath`\n"
 #                                                    "scriptpath=`dirname $scriptpath`\n"
 #                                                    "echo \"script $scriptpath\"\n"
 #                                                    "MANTIDPATH=$scriptpath/${BIN_DIR}\n"
 #                                                    "echo $MANTIDPATH\n"
-#                                                    "PV_PLUGIN_PATH=$scriptpath/${PVPLUGINS_DIR}\n"
+#                                                    "PV_PLUGIN_PATH=$scriptpath/${PVPLUGINS_DIR}/${PVPLUGINS_DIR}\n"
                                                     "PATH=$PATH:$MANTIDPATH\n"
                                                     "export MANTIDPATH PV_PLUGIN_PATH PATH\n"
 )
 
 file ( WRITE ${CMAKE_CURRENT_BINARY_DIR}/mantid.csh  "#!/bin/csh\n"
                                                     "setenv MANTIDPATH \"${CMAKE_INSTALL_PREFIX}/${BIN_DIR}\"\n"
-                                                    "setenv PV_PLUGIN_PATH \"${CMAKE_INSTALL_PREFIX}/${PVPLUGINS_DIR}\"\n"
+                                                    "setenv PV_PLUGIN_PATH \"${CMAKE_INSTALL_PREFIX}/${PVPLUGINS_DIR}/${PVPLUGINS_DIR}\"\n"
                                                     "setenv PATH \"\${PATH}:\${MANTIDPATH}\"\n"
 )
 
@@ -80,7 +80,7 @@ file ( WRITE ${CMAKE_CURRENT_BINARY_DIR}/rpm_make_links.sh "#!/bin/sh\n"
 )
 
 file ( WRITE ${CMAKE_CURRENT_BINARY_DIR}/rpm_remove_all_links.sh "#!/bin/sh\n"
-                                                             "if [ ! -f $RPM_INSTALL_PREFIX0/${PVPLUGINS_DIR}/libMantidParaViewSplatterPlotSMPlugin.so ];then\n"
+                                                             "if [ ! -f $RPM_INSTALL_PREFIX0/${PVPLUGINS_DIR}/${PVPLUGINS_DIR}/libMantidParaViewSplatterPlotSMPlugin.so ];then\n"
                                                              "  rm -f $RPM_INSTALL_PREFIX0/${BIN_DIR}/mantidplot\n"
                                                              "fi\n"
                                                              "if [ -h /etc/profile.d/mantid.sh ]; then\n"
@@ -92,7 +92,7 @@ file ( WRITE ${CMAKE_CURRENT_BINARY_DIR}/rpm_remove_all_links.sh "#!/bin/sh\n"
 )
 
 file ( WRITE ${CMAKE_CURRENT_BINARY_DIR}/rpm_remove_links.sh "#!/bin/sh\n"
-                                                             "if [ ! -f $RPM_INSTALL_PREFIX0/${PVPLUGINS_DIR}/libMantidParaViewSplatterPlotSMPlugin.so ];then\n"
+                                                             "if [ ! -f $RPM_INSTALL_PREFIX0/${PVPLUGINS_DIR}/${PVPLUGINS_DIR}/libMantidParaViewSplatterPlotSMPlugin.so ];then\n"
                                                              "  rm -f $RPM_INSTALL_PREFIX0/${BIN_DIR}/mantidplot\n"
                                                              "fi\n"
 )
diff --git a/Code/Mantid/Build/CMake/WindowsNSIS.cmake b/Code/Mantid/Build/CMake/WindowsNSIS.cmake
index e0207b48bd2148b57b7c61d7b4c72640fa398ddd..fbc7d9cb7ed9f10a79a31d6ba77aeb70bf6f6feb 100644
--- a/Code/Mantid/Build/CMake/WindowsNSIS.cmake
+++ b/Code/Mantid/Build/CMake/WindowsNSIS.cmake
@@ -84,7 +84,7 @@
 		    Push \\\"PV_PLUGIN_PATH\\\"
             Push \\\"A\\\"
             Push \\\"HKCU\\\"
-            Push \\\"$INSTDIR\\\\${PVPLUGINS_DIR}\\\"
+            Push \\\"$INSTDIR\\\\${PVPLUGINS_DIR}\\\\${PVPLUGINS_DIR}\\\"
             Call EnvVarUpdate
             Pop  \\\$0
 		
@@ -113,7 +113,7 @@
 		    Push \\\"PV_PLUGIN_PATH\\\"
             Push \\\"R\\\"
             Push \\\"HKCU\\\"
-            Push \\\"$INSTDIR\\\\${PVPLUGINS_DIR}\\\"
+            Push \\\"$INSTDIR\\\\${PVPLUGINS_DIR}\\\\${PVPLUGINS_DIR}\\\"
             Call un.EnvVarUpdate
             Pop  \\\$0
 		
diff --git a/Code/Mantid/Framework/Kernel/src/ConfigService.cpp b/Code/Mantid/Framework/Kernel/src/ConfigService.cpp
index 9373f77b15e1ccbf4e2a0998db2868df3b4b0c22..a2cd88e88d5d9b96c3ea559aeecf35138d16db3b 100644
--- a/Code/Mantid/Framework/Kernel/src/ConfigService.cpp
+++ b/Code/Mantid/Framework/Kernel/src/ConfigService.cpp
@@ -1367,13 +1367,13 @@ bool ConfigServiceImpl::isNetworkDrive(const std::string & path)
 void ConfigServiceImpl::setParaViewPluginPath() const
 {
   std::string mantid_loc = this->getDirectoryOfExecutable();
-  Poco::Path pv_plugin_path(mantid_loc + "/pvplugins");
+  Poco::Path pv_plugin_path(mantid_loc + "/pvplugins/pvplugins");
   pv_plugin_path = pv_plugin_path.absolute();
   Poco::File pv_plugin(pv_plugin_path.toString());
   if (!pv_plugin.exists() || !pv_plugin.isDirectory())
   {
     g_log.debug("ParaView plugin directory \"" + pv_plugin.path() + "\" does not exist");
-    pv_plugin_path = Poco::Path(mantid_loc + "/../pvplugins");
+    pv_plugin_path = Poco::Path(mantid_loc + "/../pvplugins/pvplugins");
     pv_plugin_path = pv_plugin_path.absolute();
     pv_plugin = Poco::File(pv_plugin_path.toString());
     if (!pv_plugin.exists() || !pv_plugin.isDirectory())
diff --git a/Code/Mantid/Vates/ParaviewPlugins/ParaViewFilters/MDEWRebinningCutterOperator/CMakeLists.txt b/Code/Mantid/Vates/ParaviewPlugins/ParaViewFilters/MDEWRebinningCutterOperator/CMakeLists.txt
index be004d1456660d8389fdadc7736c72dcf77d308e..4ef31c801cb6ed81e73ace550b257611d30033e1 100644
--- a/Code/Mantid/Vates/ParaviewPlugins/ParaViewFilters/MDEWRebinningCutterOperator/CMakeLists.txt
+++ b/Code/Mantid/Vates/ParaviewPlugins/ParaViewFilters/MDEWRebinningCutterOperator/CMakeLists.txt
@@ -15,7 +15,7 @@ target_link_libraries( MantidParaViewMDEWRebinningCutterSMPlugin
 ${MANTID_SUBPROJECT_LIBS} )
 
 # Put library into subfolder.
-SET_TARGET_OUTPUT_DIRECTORY(MantidParaViewMDEWRebinningCutterSMPlugin  ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/${CMAKE_CFG_INTDIR}/${PVPLUGINS_DIR})
+SET_TARGET_OUTPUT_DIRECTORY(MantidParaViewMDEWRebinningCutterSMPlugin  ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/${CMAKE_CFG_INTDIR}/${PVPLUGINS_DIR}/${PVPLUGINS_DIR})
 
-install( TARGETS MantidParaViewMDEWRebinningCutterSMPlugin ${TARGET_TYPE} DESTINATION ${PVPLUGINS_DIR} )
+install( TARGETS MantidParaViewMDEWRebinningCutterSMPlugin ${TARGET_TYPE} DESTINATION ${PVPLUGINS_DIR}/${PVPLUGINS_DIR} )
 
diff --git a/Code/Mantid/Vates/ParaviewPlugins/ParaViewFilters/RebinningTransformOperator/CMakeLists.txt b/Code/Mantid/Vates/ParaviewPlugins/ParaViewFilters/RebinningTransformOperator/CMakeLists.txt
index be6ec22c99708c972056646350e72eb8b13cac78..dc782e3a742f571bb908de4ff3e55da85dd37a64 100644
--- a/Code/Mantid/Vates/ParaviewPlugins/ParaViewFilters/RebinningTransformOperator/CMakeLists.txt
+++ b/Code/Mantid/Vates/ParaviewPlugins/ParaViewFilters/RebinningTransformOperator/CMakeLists.txt
@@ -14,7 +14,7 @@ target_link_libraries( MantidParaViewRebinningTransformSMPlugin
 ${MANTID_SUBPROJECT_LIBS} )
 
 # Put library into subfolder.
-SET_TARGET_OUTPUT_DIRECTORY(MantidParaViewRebinningTransformSMPlugin  ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/${CMAKE_CFG_INTDIR}/${PVPLUGINS_DIR})
+SET_TARGET_OUTPUT_DIRECTORY(MantidParaViewRebinningTransformSMPlugin  ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/${CMAKE_CFG_INTDIR}/${PVPLUGINS_DIR}/${PVPLUGINS_DIR})
 
-install( TARGETS MantidParaViewRebinningTransformSMPlugin ${TARGET_TYPE} DESTINATION ${PVPLUGINS_DIR} )
+install( TARGETS MantidParaViewRebinningTransformSMPlugin ${TARGET_TYPE} DESTINATION ${PVPLUGINS_DIR}/${PVPLUGINS_DIR} )
 
diff --git a/Code/Mantid/Vates/ParaviewPlugins/ParaViewFilters/ScaleWorkspace/CMakeLists.txt b/Code/Mantid/Vates/ParaviewPlugins/ParaViewFilters/ScaleWorkspace/CMakeLists.txt
index 0f4cba7ea14b252fb232550e1aafb992fda72073..a7771153ad5bea33ac026500f60815e0fcba0cbe 100644
--- a/Code/Mantid/Vates/ParaviewPlugins/ParaViewFilters/ScaleWorkspace/CMakeLists.txt
+++ b/Code/Mantid/Vates/ParaviewPlugins/ParaViewFilters/ScaleWorkspace/CMakeLists.txt
@@ -7,6 +7,6 @@ GUI_RESOURCE_FILES ScaleWorkspaceGUI.xml)
 # Add to the 'VatesParaViewPlugins' group in VS
 set_property( TARGET MantidParaViewScaleWorkspaceSMPlugin PROPERTY FOLDER "MantidVatesParaViewPlugins")
 # Put library into subfolder.
-SET_TARGET_OUTPUT_DIRECTORY(MantidParaViewScaleWorkspaceSMPlugin  ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/${CMAKE_CFG_INTDIR}/${PVPLUGINS_DIR})
+SET_TARGET_OUTPUT_DIRECTORY(MantidParaViewScaleWorkspaceSMPlugin  ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/${CMAKE_CFG_INTDIR}/${PVPLUGINS_DIR}/${PVPLUGINS_DIR})
 
-install( TARGETS MantidParaViewScaleWorkspaceSMPlugin ${TARGET_TYPE} DESTINATION ${PVPLUGINS_DIR})
+install( TARGETS MantidParaViewScaleWorkspaceSMPlugin ${TARGET_TYPE} DESTINATION ${PVPLUGINS_DIR}/${PVPLUGINS_DIR})
diff --git a/Code/Mantid/Vates/ParaviewPlugins/ParaViewFilters/SplatterPlot/CMakeLists.txt b/Code/Mantid/Vates/ParaviewPlugins/ParaViewFilters/SplatterPlot/CMakeLists.txt
index b1832f444289673745d8a43f45634ea6518b3c1a..34e449840a3bbebeb1a80d312fd02e04cebb8953 100644
--- a/Code/Mantid/Vates/ParaviewPlugins/ParaViewFilters/SplatterPlot/CMakeLists.txt
+++ b/Code/Mantid/Vates/ParaviewPlugins/ParaViewFilters/SplatterPlot/CMakeLists.txt
@@ -13,7 +13,7 @@ target_link_libraries( MantidParaViewSplatterPlotSMPlugin
 ${MANTID_SUBPROJECT_LIBS} )
 
 # Put library into subfolder.
-SET_TARGET_OUTPUT_DIRECTORY(MantidParaViewSplatterPlotSMPlugin ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/${CMAKE_CFG_INTDIR}/${PVPLUGINS_DIR})
+SET_TARGET_OUTPUT_DIRECTORY(MantidParaViewSplatterPlotSMPlugin ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/${CMAKE_CFG_INTDIR}/${PVPLUGINS_DIR}/${PVPLUGINS_DIR})
 
-install( TARGETS MantidParaViewSplatterPlotSMPlugin ${TARGET_TYPE} DESTINATION ${PVPLUGINS_DIR} )
+install( TARGETS MantidParaViewSplatterPlotSMPlugin ${TARGET_TYPE} DESTINATION ${PVPLUGINS_DIR}/${PVPLUGINS_DIR} )
 
diff --git a/Code/Mantid/Vates/ParaviewPlugins/ParaViewReaders/EventNexusReader/CMakeLists.txt b/Code/Mantid/Vates/ParaviewPlugins/ParaViewReaders/EventNexusReader/CMakeLists.txt
index f4e0e4e15552039b1553e5b068eca02d49cbd13d..c8685c4411036b7203f611e9b8a48e1e1098f338 100644
--- a/Code/Mantid/Vates/ParaviewPlugins/ParaViewReaders/EventNexusReader/CMakeLists.txt
+++ b/Code/Mantid/Vates/ParaviewPlugins/ParaViewReaders/EventNexusReader/CMakeLists.txt
@@ -13,8 +13,8 @@ target_link_libraries( MantidParaViewEventNexusReaderSMPlugin
 ${MANTID_SUBPROJECT_LIBS} )
 
 # Put library into subfolder.
-SET_TARGET_OUTPUT_DIRECTORY(MantidParaViewEventNexusReaderSMPlugin ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/${CMAKE_CFG_INTDIR}/${PVPLUGINS_DIR})
+SET_TARGET_OUTPUT_DIRECTORY(MantidParaViewEventNexusReaderSMPlugin ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/${CMAKE_CFG_INTDIR}/${PVPLUGINS_DIR}/${PVPLUGINS_DIR})
 
-install( TARGETS MantidParaViewEventNexusReaderSMPlugin ${TARGET_TYPE} DESTINATION ${PVPLUGINS_DIR} )
+install( TARGETS MantidParaViewEventNexusReaderSMPlugin ${TARGET_TYPE} DESTINATION ${PVPLUGINS_DIR}/${PVPLUGINS_DIR} )
 
 
diff --git a/Code/Mantid/Vates/ParaviewPlugins/ParaViewReaders/MDEWNexusReader/CMakeLists.txt b/Code/Mantid/Vates/ParaviewPlugins/ParaViewReaders/MDEWNexusReader/CMakeLists.txt
index 17656472ff807b225d0064865bd0ba07597b878a..e77ed778d553eb60331b75578b794842472f1611 100644
--- a/Code/Mantid/Vates/ParaviewPlugins/ParaViewReaders/MDEWNexusReader/CMakeLists.txt
+++ b/Code/Mantid/Vates/ParaviewPlugins/ParaViewReaders/MDEWNexusReader/CMakeLists.txt
@@ -13,8 +13,8 @@ target_link_libraries( MantidParaViewMDEWNexusReaderSMPlugin
 ${MANTID_SUBPROJECT_LIBS} )
 
 # Put library into subfolder.
-SET_TARGET_OUTPUT_DIRECTORY(MantidParaViewMDEWNexusReaderSMPlugin ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/${CMAKE_CFG_INTDIR}/${PVPLUGINS_DIR})
+SET_TARGET_OUTPUT_DIRECTORY(MantidParaViewMDEWNexusReaderSMPlugin ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/${CMAKE_CFG_INTDIR}/${PVPLUGINS_DIR}/${PVPLUGINS_DIR})
 
-install( TARGETS MantidParaViewMDEWNexusReaderSMPlugin ${TARGET_TYPE} DESTINATION ${PVPLUGINS_DIR} )
+install( TARGETS MantidParaViewMDEWNexusReaderSMPlugin ${TARGET_TYPE} DESTINATION ${PVPLUGINS_DIR}/${PVPLUGINS_DIR} )
 
 
diff --git a/Code/Mantid/Vates/ParaviewPlugins/ParaViewReaders/PeaksReader/CMakeLists.txt b/Code/Mantid/Vates/ParaviewPlugins/ParaViewReaders/PeaksReader/CMakeLists.txt
index 06da2832d51b0e083b8b8679c8dd16c0892df51b..f66ee96cfa43b38300ea4a452062af4186dce58e 100644
--- a/Code/Mantid/Vates/ParaviewPlugins/ParaViewReaders/PeaksReader/CMakeLists.txt
+++ b/Code/Mantid/Vates/ParaviewPlugins/ParaViewReaders/PeaksReader/CMakeLists.txt
@@ -13,8 +13,8 @@ target_link_libraries( MantidParaViewPeaksReaderSMPlugin
 ${MANTID_SUBPROJECT_LIBS} )
 
 # Put library into subfolder.
-SET_TARGET_OUTPUT_DIRECTORY(MantidParaViewPeaksReaderSMPlugin ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/${CMAKE_CFG_INTDIR}/${PVPLUGINS_DIR})
+SET_TARGET_OUTPUT_DIRECTORY(MantidParaViewPeaksReaderSMPlugin ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/${CMAKE_CFG_INTDIR}/${PVPLUGINS_DIR}/${PVPLUGINS_DIR})
 
-install( TARGETS MantidParaViewPeaksReaderSMPlugin ${TARGET_TYPE} DESTINATION ${PVPLUGINS_DIR} )
+install( TARGETS MantidParaViewPeaksReaderSMPlugin ${TARGET_TYPE} DESTINATION ${PVPLUGINS_DIR}/${PVPLUGINS_DIR} )
 
 
diff --git a/Code/Mantid/Vates/ParaviewPlugins/ParaViewReaders/SQWEventReader/CMakeLists.txt b/Code/Mantid/Vates/ParaviewPlugins/ParaViewReaders/SQWEventReader/CMakeLists.txt
index 52a4955713f69a852269cda98d47eaf28537109e..03516a1c39cbc4167acd77a8944be5bdf2cd043f 100644
--- a/Code/Mantid/Vates/ParaviewPlugins/ParaViewReaders/SQWEventReader/CMakeLists.txt
+++ b/Code/Mantid/Vates/ParaviewPlugins/ParaViewReaders/SQWEventReader/CMakeLists.txt
@@ -13,8 +13,8 @@ target_link_libraries( MantidParaViewSQWEventReaderSMPlugin
 ${MANTID_SUBPROJECT_LIBS} )
 
 # Put library into subfolder.
-SET_TARGET_OUTPUT_DIRECTORY(MantidParaViewSQWEventReaderSMPlugin ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/${CMAKE_CFG_INTDIR}/${PVPLUGINS_DIR})
+SET_TARGET_OUTPUT_DIRECTORY(MantidParaViewSQWEventReaderSMPlugin ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/${CMAKE_CFG_INTDIR}/${PVPLUGINS_DIR}/${PVPLUGINS_DIR})
 
-install( TARGETS MantidParaViewSQWEventReaderSMPlugin ${TARGET_TYPE} DESTINATION ${PVPLUGINS_DIR} )
+install( TARGETS MantidParaViewSQWEventReaderSMPlugin ${TARGET_TYPE} DESTINATION ${PVPLUGINS_DIR}/${PVPLUGINS_DIR} )
 
 
diff --git a/Code/Mantid/Vates/ParaviewPlugins/ParaViewReaders/SQWReader/CMakeLists.txt b/Code/Mantid/Vates/ParaviewPlugins/ParaViewReaders/SQWReader/CMakeLists.txt
index 554e60d2447282d93044d552bd3bbf55a2e139ae..b7fa6c5efbbf03aada97290476af3fe883efc440 100644
--- a/Code/Mantid/Vates/ParaviewPlugins/ParaViewReaders/SQWReader/CMakeLists.txt
+++ b/Code/Mantid/Vates/ParaviewPlugins/ParaViewReaders/SQWReader/CMakeLists.txt
@@ -13,9 +13,9 @@ target_link_libraries( MantidParaViewSQWReaderSMPlugin
 ${MANTID_SUBPROJECT_LIBS} )
 
 # Put library into subfolder.
-SET_TARGET_OUTPUT_DIRECTORY( MantidParaViewSQWReaderSMPlugin ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/${CMAKE_CFG_INTDIR}/${PVPLUGINS_DIR})
+SET_TARGET_OUTPUT_DIRECTORY( MantidParaViewSQWReaderSMPlugin ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/${CMAKE_CFG_INTDIR}/${PVPLUGINS_DIR}/${PVPLUGINS_DIR})
 
-install( TARGETS MantidParaViewSQWReaderSMPlugin ${TARGET_TYPE} DESTINATION ${PVPLUGINS_DIR} )
+install( TARGETS MantidParaViewSQWReaderSMPlugin ${TARGET_TYPE} DESTINATION ${PVPLUGINS_DIR}/${PVPLUGINS_DIR} )
 
 
 
diff --git a/Code/Mantid/Vates/ParaviewPlugins/ParaViewSources/MDEWSource/CMakeLists.txt b/Code/Mantid/Vates/ParaviewPlugins/ParaViewSources/MDEWSource/CMakeLists.txt
index 42e0582fa9c830dfe535b1120807217ff893779d..8666aef34c7ee8e4be66763a5d45285e23d8466b 100644
--- a/Code/Mantid/Vates/ParaviewPlugins/ParaViewSources/MDEWSource/CMakeLists.txt
+++ b/Code/Mantid/Vates/ParaviewPlugins/ParaViewSources/MDEWSource/CMakeLists.txt
@@ -11,6 +11,6 @@ target_link_libraries( MantidParaViewMDEWSourceSMPlugin
 ${MANTID_SUBPROJECT_LIBS} )
 
 # Put library into subfolder.
-SET_TARGET_OUTPUT_DIRECTORY(MantidParaViewMDEWSourceSMPlugin ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/${CMAKE_CFG_INTDIR}/${PVPLUGINS_DIR})
+SET_TARGET_OUTPUT_DIRECTORY(MantidParaViewMDEWSourceSMPlugin ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/${CMAKE_CFG_INTDIR}/${PVPLUGINS_DIR}/${PVPLUGINS_DIR})
 
-install( TARGETS MantidParaViewMDEWSourceSMPlugin ${TARGET_TYPE} DESTINATION ${PVPLUGINS_DIR} )
+install( TARGETS MantidParaViewMDEWSourceSMPlugin ${TARGET_TYPE} DESTINATION ${PVPLUGINS_DIR}/${PVPLUGINS_DIR} )
diff --git a/Code/Mantid/Vates/ParaviewPlugins/ParaViewSources/MDHWSource/CMakeLists.txt b/Code/Mantid/Vates/ParaviewPlugins/ParaViewSources/MDHWSource/CMakeLists.txt
index 084a99050d0e1a70d120c86084bb05c1dcffb595..8abc50b36fd6a685c4361d77700633ae1d4607e7 100644
--- a/Code/Mantid/Vates/ParaviewPlugins/ParaViewSources/MDHWSource/CMakeLists.txt
+++ b/Code/Mantid/Vates/ParaviewPlugins/ParaViewSources/MDHWSource/CMakeLists.txt
@@ -11,6 +11,6 @@ target_link_libraries( MantidParaViewMDHWSourceSMPlugin
 ${MANTID_SUBPROJECT_LIBS} )
 
 # Put library into subfolder.
-SET_TARGET_OUTPUT_DIRECTORY(MantidParaViewMDHWSourceSMPlugin ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/${CMAKE_CFG_INTDIR}/${PVPLUGINS_DIR})
+SET_TARGET_OUTPUT_DIRECTORY(MantidParaViewMDHWSourceSMPlugin ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/${CMAKE_CFG_INTDIR}/${PVPLUGINS_DIR}/${PVPLUGINS_DIR})
 
-install( TARGETS MantidParaViewMDHWSourceSMPlugin ${TARGET_TYPE} DESTINATION ${PVPLUGINS_DIR} )
+install( TARGETS MantidParaViewMDHWSourceSMPlugin ${TARGET_TYPE} DESTINATION ${PVPLUGINS_DIR}/${PVPLUGINS_DIR} )
diff --git a/Code/Mantid/Vates/ParaviewPlugins/ParaViewSources/PeaksSource/CMakeLists.txt b/Code/Mantid/Vates/ParaviewPlugins/ParaViewSources/PeaksSource/CMakeLists.txt
index 874c04c3dde0bb4ae2ff81dad326f04538c087b1..f1d34d87f11a84a77f7263736709320b0bc3903c 100644
--- a/Code/Mantid/Vates/ParaviewPlugins/ParaViewSources/PeaksSource/CMakeLists.txt
+++ b/Code/Mantid/Vates/ParaviewPlugins/ParaViewSources/PeaksSource/CMakeLists.txt
@@ -11,6 +11,6 @@ target_link_libraries( MantidParaViewPeaksSourceSMPlugin
 ${MANTID_SUBPROJECT_LIBS} )
 
 # Put library into subfolder.
-SET_TARGET_OUTPUT_DIRECTORY(MantidParaViewPeaksSourceSMPlugin ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/${CMAKE_CFG_INTDIR}/${PVPLUGINS_DIR})
+SET_TARGET_OUTPUT_DIRECTORY(MantidParaViewPeaksSourceSMPlugin ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/${CMAKE_CFG_INTDIR}/${PVPLUGINS_DIR}/${PVPLUGINS_DIR})
 
-install( TARGETS MantidParaViewPeaksSourceSMPlugin ${TARGET_TYPE} DESTINATION ${PVPLUGINS_DIR} )
+install( TARGETS MantidParaViewPeaksSourceSMPlugin ${TARGET_TYPE} DESTINATION ${PVPLUGINS_DIR}/${PVPLUGINS_DIR} )
diff --git a/Code/Mantid/Vates/ParaviewPlugins/ParaViewWidgets/RebinningCutterObjectPanel/CMakeLists.txt b/Code/Mantid/Vates/ParaviewPlugins/ParaViewWidgets/RebinningCutterObjectPanel/CMakeLists.txt
index 2ed508f487fdc5959f4d0029623d9f9b07de727f..9d8d4191a2bca56b2833e753728723bc8b4a6221 100644
--- a/Code/Mantid/Vates/ParaviewPlugins/ParaViewWidgets/RebinningCutterObjectPanel/CMakeLists.txt
+++ b/Code/Mantid/Vates/ParaviewPlugins/ParaViewWidgets/RebinningCutterObjectPanel/CMakeLists.txt
@@ -19,8 +19,8 @@ target_link_libraries( MantidParaViewRebinningCutterObjectPanel
 MantidParaViewQtWidgets )
 
 # Put library into subfolder.
-SET_TARGET_OUTPUT_DIRECTORY( MantidParaViewRebinningCutterObjectPanel  ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/${CMAKE_CFG_INTDIR}/${PVPLUGINS_DIR})
+SET_TARGET_OUTPUT_DIRECTORY( MantidParaViewRebinningCutterObjectPanel  ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/${CMAKE_CFG_INTDIR}/${PVPLUGINS_DIR}/${PVPLUGINS_DIR})
 
-install( TARGETS MantidParaViewRebinningCutterObjectPanel ${TARGET_TYPE} DESTINATION ${PVPLUGINS_DIR} )
+install( TARGETS MantidParaViewRebinningCutterObjectPanel ${TARGET_TYPE} DESTINATION ${PVPLUGINS_DIR}/${PVPLUGINS_DIR} )
 
 
diff --git a/Code/Mantid/Vates/ParaviewPlugins/ParaViewWidgets/RebinningTransformObjectPanel/CMakeLists.txt b/Code/Mantid/Vates/ParaviewPlugins/ParaViewWidgets/RebinningTransformObjectPanel/CMakeLists.txt
index 58f4704e693a9f8526543d2bfb49902037fba968..685736014f3b1b02d1aad7ea33bdd5fba777d39d 100644
--- a/Code/Mantid/Vates/ParaviewPlugins/ParaViewWidgets/RebinningTransformObjectPanel/CMakeLists.txt
+++ b/Code/Mantid/Vates/ParaviewPlugins/ParaViewWidgets/RebinningTransformObjectPanel/CMakeLists.txt
@@ -19,8 +19,8 @@ target_link_libraries( MantidParaViewRebinningTransformObjectPanel
 MantidParaViewQtWidgets )
 
 # Put library into subfolder.
-SET_TARGET_OUTPUT_DIRECTORY( MantidParaViewRebinningTransformObjectPanel  ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/${CMAKE_CFG_INTDIR}/${PVPLUGINS_DIR})
+SET_TARGET_OUTPUT_DIRECTORY( MantidParaViewRebinningTransformObjectPanel  ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/${CMAKE_CFG_INTDIR}/${PVPLUGINS_DIR}/${PVPLUGINS_DIR})
 
-install( TARGETS MantidParaViewRebinningTransformObjectPanel ${TARGET_TYPE} DESTINATION ${PVPLUGINS_DIR} )
+install( TARGETS MantidParaViewRebinningTransformObjectPanel ${TARGET_TYPE} DESTINATION ${PVPLUGINS_DIR}/${PVPLUGINS_DIR} )
 
 
diff --git a/Code/Mantid/Vates/VatesSimpleGui/StandAloneExec/CMakeLists.txt b/Code/Mantid/Vates/VatesSimpleGui/StandAloneExec/CMakeLists.txt
index e2ae33de92c92db1aa0e0f02db8fb9d4cc02b0d0..e3b94dab2d016a4550ac32d0be042d0252c4efc3 100644
--- a/Code/Mantid/Vates/VatesSimpleGui/StandAloneExec/CMakeLists.txt
+++ b/Code/Mantid/Vates/VatesSimpleGui/StandAloneExec/CMakeLists.txt
@@ -52,7 +52,7 @@ if( SQUISH_FOUND )
   set( auto_test_dir ${CMAKE_SOURCE_DIR} )
   string( REGEX REPLACE "Code/Mantid" "Test/AutoTestData" auto_test_dir ${auto_test_dir} )
   set( SQUISH_ENV_VARS
-    PV_PLUGIN_PATH=$<TARGET_FILE_DIR:${SQUISH_AUT}>/${PVPLUGINS_DIR}
+    PV_PLUGIN_PATH=$<TARGET_FILE_DIR:${SQUISH_AUT}>/${PVPLUGINS_DIR}/${PVPLUGINS_DIR}
     MANTID_AUTOTEST_DATA=${auto_test_dir}
     SQUISH_SCRIPT_DIR=${VSI_GLOBAL_SCRIPTS}
   )
diff --git a/Code/Mantid/Vates/VatesSimpleGui/ViewWidgets/CMakeLists.txt b/Code/Mantid/Vates/VatesSimpleGui/ViewWidgets/CMakeLists.txt
index 806f195f3ed626b9545c5ecde5052c6ea7d7cf79..75e635b57fdc179211e15eb983c7ee85391cbdb8 100644
--- a/Code/Mantid/Vates/VatesSimpleGui/ViewWidgets/CMakeLists.txt
+++ b/Code/Mantid/Vates/VatesSimpleGui/ViewWidgets/CMakeLists.txt
@@ -105,7 +105,7 @@ if( SQUISH_FOUND )
 
   # Need to set environmental variables next
   set( SQUISH_ENV_VARS
-    PV_PLUGIN_PATH=$<TARGET_FILE_DIR:${SQUISH_AUT}>/${PVPLUGINS_DIR}
+    PV_PLUGIN_PATH=$<TARGET_FILE_DIR:${SQUISH_AUT}>/${PVPLUGINS_DIR}/${PVPLUGINS_DIR}
     SCRIPTS_DIR=${CMAKE_CURRENT_SOURCE_DIR}/test/mp_scripts
     SQUISH_SCRIPT_DIR=${VSI_GLOBAL_SCRIPTS}:${CMAKE_CURRENT_SOURCE_DIR}/test/common/scripts
   )