@jtodd76
I'm using this little converter called ShanaEncoder ... super easy to use... you just drag the files in...and over on the right choose the preset called "copy" and then "stream copy to MP4" then choose your output where you want the files to go and click start.... doesn't re-encode anything... Just copies it... I recently had a series with 130 eps that were all red...changing to an mp4 container totally fixed it....but only if it's direct playing....if you ever direct stream it...it Plex will wrap it into an MKV container and thus the bug will reappear....Now if the audio is something that Plex has to transcode instead of direct play that might screw things up.... but luckily most of my files are stereo and not multi-channel....so I never run into the issue of Plex having to transcode audio....
https://sourceforge.net/projects/shanaencoder/
