I'm not sure what the limitations are, but I had an MKV file with 20 streams (1 video, 3 audio, 16 subtitle tracks) that would stop the file scanner. Everything found before that file would be available via the program but anything after (and including that particular file) would not be served.
I remuxed the file using mkvtoolnix, keeping all the streams the same, and still had problems. I remuxed the file keeping the video, audio and only ONE subtitle track and the program resumed normal operation. I don't have time, right now, to figure out how many streams is too many but I thought that I would let everyone know.
It is only a minor bug so I don't expect it to get fixed anytime soon.