There was a file extension case issue, yeah… but I had it in my head that that didn’t make it not show up in the database, just wouldn’t play, IIRC.
Can you identify any of the missing ones? If you could, that might help.
The other thing you could do is delete your songs.gdb, and run it at -d5. See if you see any errors in the log about not being able to stat the file, or some other error.