No, songs are on the same physical disk and the same logical partition.
Is there a specific reason you can’t run nightlies? I can help troubleshoot this with 0.2.4 if you want, but I’m pretty sure that nightlies would Just Work ™.
If you need/want to continue running 0.2.4, though, the thing to do is put a logfile in your config, delete the songs.gdb, and run mt-daapd with -d9. Connect to the server and get at least one example (with filename, etc) of a duplicated song and a missing song.
Then zip up the generated log file and mail it to me at “ron at pedde.com”. Give the the details on what’s missing and what’s duped, and I’ll look through the log file and try to find out why.