diff --git a/Code/Mantid/Build/CMake/WindowsNSIS.cmake b/Code/Mantid/Build/CMake/WindowsNSIS.cmake
index 03b5c74cff824b22c44394cd66783478531aaf7d..4bf5d6d7200447ab9622a0985f097cf0cf1dcf01 100644
--- a/Code/Mantid/Build/CMake/WindowsNSIS.cmake
+++ b/Code/Mantid/Build/CMake/WindowsNSIS.cmake
@@ -34,9 +34,6 @@
     install ( DIRECTORY ${CMAKE_LIBRARY_PATH}/Python27/Scripts DESTINATION bin PATTERN ".svn" EXCLUDE PATTERN ".git" EXCLUDE )
     install ( FILES ${PY_DLL_PREFIX}${PY_DLL_SUFFIX_RELEASE} ${PYTHON_EXECUTABLE} ${PYTHONW_EXECUTABLE} DESTINATION bin )
 
-    install ( DIRECTORY ${CMAKE_LIBRARY_PATH}/qt_plugins/imageformats DESTINATION plugins/qtplugins PATTERN ".svn" EXCLUDE PATTERN ".git" EXCLUDE )
-    install ( FILES ${CMAKE_CURRENT_SOURCE_DIR}/Installers/WinInstaller/qt.conf DESTINATION bin )
-    
     # include files
     install ( DIRECTORY ${CMAKE_INCLUDE_PATH}/boost DESTINATION include PATTERN ".svn" EXCLUDE PATTERN ".git" EXCLUDE )
     install ( DIRECTORY ${CMAKE_INCLUDE_PATH}/Poco DESTINATION include PATTERN ".svn" EXCLUDE PATTERN ".git" EXCLUDE )
@@ -105,6 +102,14 @@
     REGEX "(QtDesigner4.dll)|(QtDesignerComponents4.dll)|(QtScript4.dll)|(-gd-)|(d4.dll)|(_d.dll)" 
     EXCLUDE 
     PATTERN ".git" EXCLUDE )
+
+    # Qt plugins into out plugins directory and use qt.conf to point Qt at where they are
+    install ( DIRECTORY ${CMAKE_LIBRARY_PATH}/qt_plugins/imageformats ${CMAKE_LIBRARY_PATH}/qt_plugins/sqldrivers DESTINATION plugins/qtplugins 
+              REGEX "^.*d4.dll$" EXCLUDE  )
+    install ( FILES ${CMAKE_CURRENT_SOURCE_DIR}/Installers/WinInstaller/qt.conf DESTINATION bin )
+   
+    # Copy assistant.exe
+    install ( FILES ${CMAKE_LIBRARY_PATH}/assistant.exe DESTINATION bin )
     
     # Release deployments do modify enviromental variables, other deployments do not.
     if(CPACK_PACKAGE_SUFFIX STREQUAL "") 
diff --git a/Code/Mantid/docs/qtassistant/CMakeLists.txt b/Code/Mantid/docs/qtassistant/CMakeLists.txt
index 6d514ff56900d928e76719ce69da482cdb1ab9f1..e56640f3718c053c7763a283ce4dd852900e5ba4 100644
--- a/Code/Mantid/docs/qtassistant/CMakeLists.txt
+++ b/Code/Mantid/docs/qtassistant/CMakeLists.txt
@@ -4,7 +4,7 @@
 #QT_QCOLLECTIONGENERATOR_EXECUTABLE
 if (QT_QCOLLECTIONGENERATOR_EXECUTABLE)
    # set directories to follow structure of qt4 on linux
-   set (HELP_OUT_DIR ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/${CMAKE_CFG_INTDIR}/qtassistant)
+   set (HELP_OUT_DIR ${CMAKE_CURRENT_BINARY_DIR}/qtassistant)
    set (HELP_QCH_DIR ${HELP_OUT_DIR}/qch)
    set (HELP_HTML_DIR ${HELP_OUT_DIR}/html)
    set (HELP_IMG_DIR ${HELP_OUT_DIR}/src/images)
@@ -41,8 +41,6 @@ if (QT_QCOLLECTIONGENERATOR_EXECUTABLE)
       add_custom_command( OUTPUT ${CMAKE_BINARY_DIR}/${CMAKE_CFG_INTDIR}/assistant.exe
                           COMMAND ${CMAKE_COMMAND} ARGS -E copy_if_different ${THIRD_PARTY}/assistant.exe
                                   ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/${CMAKE_CFG_INTDIR}/assistant.exe )
-      install (FILES  ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/${CMAKE_CFG_INTDIR}/assistant.exe
-               DESTINATION ${CMAKE_INSTALL_PREFIX} )
    endif (WIN32)
 
    set ( HELP_ALGO_OUT
@@ -69,11 +67,21 @@ if (QT_QCOLLECTIONGENERATOR_EXECUTABLE)
                       DEPENDS ${HELP_ALGO_OUT} ${HELP_FIT_OUT} ${HELP_QHCP_SOURCE}
 		      COMMAND ${QT_QCOLLECTIONGENERATOR_EXECUTABLE} ${HELP_OUT_DIR}/mantid.qhcp
 		      )
-
+              
    add_custom_target ( qtassistant ALL
                        DEPENDS MantidPlot ${HELP_QCH_DIR}/mantid.qhc
                        )
 
+   # Copy to correct location in bin
+   set (HELP_BIN_OUT_DIR  ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/${CMAKE_CFG_INTDIR}/qtassistant )
+   add_custom_command( TARGET qtassistant
+                       POST_BUILD
+                       COMMAND ${CMAKE_COMMAND} ARGS -E copy_directory ${HELP_OUT_DIR} ${HELP_BIN_OUT_DIR} 
+                       COMMENT "Copying qtassistant to bin" )
+
+   ###########################################################################################
+   # Installation settings
+   ###########################################################################################
    set ( GUI_HELP_DEST share/doc )
 
    install ( DIRECTORY   ${HELP_QCH_DIR} ${HELP_HTML_DIR} ${HELP_IMG_DIR}