Have you (at any point) done any of the following?
- used it as a hard disk (enabled disk mode) and put data on it (and maybe even put that in trash and dissconnected before emptying trash)?
- synced iCal data?
- synced Address Book data?
If not you could just use the latest iPod updater to do a complete restore. That should get you your space back (by deleting whatever's on it)...