Subtitles

Greetings,
I've been ripping my entire DVD collection, I'm sure that's nothing new on this site, using DVDFab. When I rip the DVD I usually let it run with the default settings. Some movies have multiple subtitles (different languages, commentary & whatnot) and the software collects them and places them into 1 file. When I play them on an independent player, such as VLC, it sees both subtitles as options. Plex, however only sees one. I would like a solution that doesn't involve re-ripping a significant portion of my collection. Any help is appreciated.