Odd. Maybe that means that your disk's problem is in the scratch partition or in the database.

There's a drivebuilder image that you can use to reformat the empeg's drive to its initial state. You could download all of your mp3s to your computer first (preferably with jEmplode, as it has better features in this area) if you don't still have a copy of them on the computer first, and then reupload them. The drivebuilder is at the same place the normal software is, IIRC.