Alright, I'll try upgrading.
An interesting thing I found though, was that selecting all tracks in my library tells me I have 1922 files, but manually adding all the track counts tells me I should have 1925 files. If the tracks aren't in my library or inbox, I'm not sure where else they could be. But, I do think there are somehow some duplicate files hiding somewhere.
Thanks for your help.
Edit: Now I'm extra confused. I turned on the library explorer, and lo and behold, there are the duplicate files.
http://i.imgur.com/4YVhVkq.pngBut now the library explorer reports three files, while showing six! I can't seem to figure out where the duplicates are being stored either still.
Edit 2: Even more confusing, only the first three listings play the songs, but the names don't match up with the track. So, the first 02 plays 02, the second 02 plays 03, and the first 03 plays 04, and the rest don't play anything. No idea what's causing this.