Well, I believe I've solved the problem. I booted into bootloader USB mode, backed up my music files, then completely wiped the drive. I first loaded the most recent CVS, then initialized tagcache and enabled auto updates. Finally, I loaded my music a few gigs at a time, letting the player update the database after each bit was transferred. The database updated without a hitch every time.
If it works for PCs, I guess it works for MP3 players as well... when in doubt, clear the drive off an reinstall everything.