You can try to clean out everything by connecting to the player with something like Hyperterminal (check the FAQ for the details) and then erase all the fid files (rm /drive0/fids/* - if you have a two drive unit also do rm /drive1/fids/*) and the database file, tags file and playlist file (rm /drive0/var/database ; rm /drive0/var/tags ; rm /drive0/var/playlists).
(Or you could completely wipe the disk(s) by usig the disk builder image - after you've applied that one, don't forget to install a software .build file)

Also check out this specific FAQ for problems with multiple ID3V2 entries in the mp3 files.

/Michael