diff --git a/buildconfig/Jenkins/buildscript b/buildconfig/Jenkins/buildscript
index 86855fcc44a0e182ea979f8ca7cf1839957301a6..821f38b1d37ab26a3ec50191c5ec9300a49821a4 100755
--- a/buildconfig/Jenkins/buildscript
+++ b/buildconfig/Jenkins/buildscript
@@ -97,12 +97,12 @@ fi
 ###############################################################################
 if [[ $(uname) == 'Darwin' ]] && [[ ! $USE_CLANG ]]; then
   # Assuming we are using the Intel compiler
-  cd $WORKSPACE/Code
+  cd $WORKSPACE
   ./fetch_Third_Party.sh
   cd $WORKSPACE
   # Setup environment variables
   source /opt/intel/bin/iccvars.sh intel64
-  export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:$WORKSPACE/Code/Third_Party/lib/mac64:/Library/Frameworks
+  export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:$WORKSPACE/Third_Party/lib/mac64:/Library/Frameworks
   # Make sure we pick up the Intel compiler
   export CC=icc
   export CXX=icpc
@@ -183,7 +183,7 @@ rm -f *.dmg *.rpm *.deb *.tar.gz
 ###############################################################################
 # CMake configuration
 ###############################################################################
-$SCL_ON_RHEL6 "cmake -DCMAKE_BUILD_TYPE=${BUILD_CONFIG} -DENABLE_CPACK=ON -DMAKE_VATES=ON -DParaView_DIR=${PARAVIEW_DIR} -DMANTID_DATA_STORE=${MANTID_DATA_STORE} -DDOCS_HTML=ON ${PACKAGINGVARS} ../Code/Mantid"
+$SCL_ON_RHEL6 "cmake -DCMAKE_BUILD_TYPE=${BUILD_CONFIG} -DENABLE_CPACK=ON -DMAKE_VATES=ON -DParaView_DIR=${PARAVIEW_DIR} -DMANTID_DATA_STORE=${MANTID_DATA_STORE} -DDOCS_HTML=ON ${PACKAGINGVARS} .."
 
 ###############################################################################
 # Coverity build should exit early
@@ -260,4 +260,4 @@ fi
 ###############################################################################
 if [[ "${ON_RHEL7}" == true ]] && [[ ${JOB_NAME} == *pull_requests* ]]; then
   $SCRIPT_DIR/systemtests
-fi
+	fi
diff --git a/buildconfig/Jenkins/buildscript.bat b/buildconfig/Jenkins/buildscript.bat
index a0e9bbd0a8d276964c488e086d045ca5c4e480cf..91ec6ac846f62bc9d7144ec04f1e61cb156577da 100755
--- a/buildconfig/Jenkins/buildscript.bat
+++ b/buildconfig/Jenkins/buildscript.bat
@@ -19,7 +19,7 @@ echo %sha1%
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
 :: Get or update the third party dependencies
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
-cd %WORKSPACE%\Code
+cd %WORKSPACE%
 call fetch_Third_Party win64
 cd %WORKSPACE%
 
@@ -100,12 +100,12 @@ if not "%JOB_NAME%"=="%JOB_NAME:relwithdbg=%" (
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
 :: Update the PATH so that we can find everything
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
-set PATH=%WORKSPACE%\Code\Third_Party\lib\win64;%WORKSPACE%\Code\Third_Party\lib\win64\Python27;%WORKSPACE%\Code\Third_Party\lib\win64\mingw;%PARAVIEW_DIR%\bin\%BUILD_CONFIG%;%PATH%
+set PATH=%WORKSPACE%\Third_Party\lib\win64;%WORKSPACE%\Third_Party\lib\win64\Python27;%WORKSPACE%\Third_Party\lib\win64\mingw;%PARAVIEW_DIR%\bin\%BUILD_CONFIG%;%PATH%
 
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
 :: CMake configuration
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
-"%CMAKE_BIN_DIR%\cmake.exe" -G "Visual Studio 11 Win64" -DCONSOLE=OFF -DENABLE_CPACK=ON -DMAKE_VATES=ON -DParaView_DIR=%PARAVIEW_DIR% -DMANTID_DATA_STORE=!MANTID_DATA_STORE! -DUSE_PRECOMPILED_HEADERS=ON %PACKAGE_DOCS% ..\Code\Mantid
+"%CMAKE_BIN_DIR%\cmake.exe" -G "Visual Studio 11 Win64" -DCONSOLE=OFF -DENABLE_CPACK=ON -DMAKE_VATES=ON -DParaView_DIR=%PARAVIEW_DIR% -DMANTID_DATA_STORE=!MANTID_DATA_STORE! -DUSE_PRECOMPILED_HEADERS=ON %PACKAGE_DOCS% ..
 if ERRORLEVEL 1 exit /B %ERRORLEVEL%
 
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::