I’m also running mt-daapd 0.2.4 on Ubuntu 6.06, and I had the same problem; some songs missing, some duplicated. I tried with both rhythmbox and git as clients and it was the same way. I did what rpedde suggested, set up a log, deleted the db and ran it at -d9. So far, though, I haven’t found any duplicates or missing tracks. I’ll let you know if it comes up again.
Like the original poster, all my mp3s are on the same physical drive, on the same partition actually (a FAT32 partition).
mt-daapd is reporting the same number of tracks as before: 2869. Using the same directory for the collection report, Amarok lists 2897 tracks, but that might be unrelated.