A quick thing to check would be audio that is tiny, by default MB ignores tracks less than 20KB [MB>Edit>Edit Prefs>Library]
So you could make an auto-playlist in iTunes for small file size / duration and organise by duration, do likewise in MB and if there is a difference, voila.
Likewise any video files might mess with the number comparison.
Otherwise I think you have a game of guess who
, making auto-playlists in both which pull all songs less than a minute > check count > less than minute 30 > check count > ...
Fairly quickly you would find in what block the missing songs are, and then you can change the increment to narrow down the song duration more accurately and find the culprit.
Hope this makes sense, good hunting ^^