Agreed. The manual clearing and rebuilding should help. If rebuilding by hand does not work, there are a few shortcuts you can take that might help. This is the command structure I used when I ran into trouble with big databases and problems building them. Try the following sequence:

swapon /swapfile
rw
rwm
cd /drive0/var
rm database
rm tags
rm playlists
player
(let player rebuild databases)
(quit player)
cd /drive0/var
ls (you should see database files here)
rom
ro
swapoff
exit
(reboot)