diff --git a/Code/Mantid/Framework/Kernel/src/ConfigService.cpp b/Code/Mantid/Framework/Kernel/src/ConfigService.cpp
index 3a528e9535f688d7da25c81b243cf1fb0ef49c4f..0cdab17652bd7d4dbe4f5ee8eed37c2ed58d9099 100644
--- a/Code/Mantid/Framework/Kernel/src/ConfigService.cpp
+++ b/Code/Mantid/Framework/Kernel/src/ConfigService.cpp
@@ -672,9 +672,11 @@ void ConfigServiceImpl::updateConfig(const std::string& filename, const bool app
   loadConfig(filename, append);
 
   //Ensure that the default save directory makes sense
-  std::string save_dir = getString("defaultsave.directory");
-  if (Poco::trimInPlace(save_dir).size() == 0) {
-    setString("defaultsave.directory", Poco::Path::home());
+  if (!append)
+  {
+    std::string save_dir = getString("defaultsave.directory");
+    if (Poco::trimInPlace(save_dir).size() == 0) 
+      setString("defaultsave.directory", Poco::Path::home());
   }
 
   if (update_caches)