I realize this is an old post, but I ran into the issue today and nothing in this post resolved my problem. What did resolve the problem was simply to export the settings using the button at the bottom of the Preferences dialog. Edit the preferences.dat file created by the export and change the locations manually. When done, save the file and use the import button to bring the modified settings back in. This was particularly useful when trying to change the Templates folder, which has the edit icon faded out.