Plex Server not indexing some files in folder

I added some avi files as TV shows to my Plex server which have the following file structure:

Family Guy
    Family Guy - Season 1
        Family Guy [1.01] Death Has a Shadow.avi
        Family Guy [1.02] I Never Met the Dead Man.avi
        ...
    Family Guy - Season 2
        Family Guy [2.01] Peter, Peter, Caviar Eater.avi
        Family Guy [2.02] Holy Crap.avi
        ...
    ...

Plex has indexed some episodes in some seasons, but it's missing a lot of episodes and in some cases entire seasons. The permissions for every file are 644 so they can be read by anyone, and the directory permissions are all 755 so can be executed by anyone.

I've read through a lot of forum posts with similar issues which were resolved by changing the permissions, or an issue with the way the files are named, but those solutions didn't help me because the file permissions and naming convention are the same for files Plex has indexed as for those it hasn't.

I can play all of the files it hasn't indexed using VLC on Ubuntu Desktop 14.04 and Windows 10, and Windows Media Player so I think that rules out anything to do with the files being corrupted.

Does anyone know what else could be causing Plex not to index those files and what I can do to fix it?