I had this same problem. I had way to many misplaced files to try and move everything back to wher it belongs I just ran the Disk Builder and I am currently reloading all my tunes. The Directory structure on my PC is in great shape so it is just easier this way. I just didn't feel like sitting around moving files in Emplode for hours on end. At least now it will load all the songs correctly without any help from me(for the most part).