I think I saw it somewhere that MKV wasn't supported yet in plex.
Perhaps it's because i'm in the Preview Program, but my MKVs are playing perfectly though plex (1080p, dual audio, etc...)
However, for some MKVs, when switching audio tracks, things seem to mess up after that.
The first time i choose the alternate audio track, nothing happens. The second time, the audio does successfully switch, but then the playback controls disappear (pressing A, no longer works) and soon after the video stops.
But again, this is only for some...most are playing fine
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Also...
Pausing a video for about 10-15 minutes and then resuming...seems to continue for a few seconds and the the screen goes black
Stopping the video and then resuming, picks up where it left off very nicely...however, it reverts back to using the first audio stream instead of the last used audio stream
Note: I was using an MKV so i'm not sure if it applies to all containers