diff --git a/buildconfig/Jenkins/buildscript b/buildconfig/Jenkins/buildscript
index a5b7c34ce139dcf5881b657b3a4312fae388f244..a006be8a825928cb895953cb22c2aa1c1f021ce3 100755
--- a/buildconfig/Jenkins/buildscript
+++ b/buildconfig/Jenkins/buildscript
@@ -300,10 +300,13 @@ fi
 ###############################################################################
 # Run the unit tests
 ###############################################################################
+# Prevent race conditions when creating the user config directory
+userconfig_dir=$HOME/.mantid
+rm -fr $userconfig_dir
+mkdir -p $userconfig_dir
+touch $userconfig_dir/Mantid.user.properties
+
 if [[ ${DO_UNITTESTS} == true ]]; then
-  # Remove any Mantid.user.properties file
-  userprops=~/.mantid/Mantid.user.properties
-  rm -f $userprops
   $CTEST_EXE -j${BUILD_THREADS:?} --schedule-random --output-on-failure
 fi
 
diff --git a/buildconfig/Jenkins/buildscript.bat b/buildconfig/Jenkins/buildscript.bat
index 190353049b998d219c7e23b432989b6a18e8b6b6..78194f3dbbf57d5f7909c5a4042e10b270e8a1f8 100755
--- a/buildconfig/Jenkins/buildscript.bat
+++ b/buildconfig/Jenkins/buildscript.bat
@@ -157,10 +157,14 @@ if ERRORLEVEL 1 exit /B %ERRORLEVEL%
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
 :: Run the tests
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
-:: Remove the user properties file just in case anything polluted it
+:: Remove any user configuration and create a blank user properties file
+:: This prevents race conditions when creating the user config directory
 set USERPROPS=bin\%BUILD_CONFIG%\Mantid.user.properties
 del %USERPROPS%
-
+set CONFIGDIR=%APPDATA%\mantidproject\mantid
+rmdir /S /Q %CONFIGDIR%
+mkdir %CONFIGDIR%
+call cmake.exe -E touch %USERPROPS%
 call ctest.exe -C %BUILD_CONFIG% -j%BUILD_THREADS% --schedule-random --output-on-failure
 if ERRORLEVEL 1 exit /B %ERRORLEVEL%