I’ve been recording a bunch of kids movies (and then converting them to h.264 MP4), and have noticed that small minority are being listed as only having AC3 Stereo audio (even though they actually have AC3 5.1 tracks). MediaInfo does show them as having AC3 5.1, and Handbrake also sees the 5.1 track (and passes it through natively to the MP4). Plex sees the correct AC3 5.1 track in the converted MP4 perfectly fine. Since I’m just recording them for later viewing, I haven’t actually played the original .TS recordings to see if my receiver actually picks up the 5.1 track from Plex or not.
Not sure if this is an issue with Plex or the original broadcast format. I’m assuming the former, since MediaInfo and Handbrake don’t have an issue with the .TS file.
With some broadcast channels, the 5.1 audio doesn’t appear to be broadcast all of the time - it kicks in for specific shows and programmes. Plex seems to only use the audio tracks it can detect at the beginning of a file - so if your recording starts at the end of a previous programme that has only 2-channel audio - that’s the only choice you’ll get.
The short term work around appears to be convert the file outside of Plex, or snip the first bit of the ts file off (using dd or something similar). As long as Plex can find the 5.1 audio track at the beginning of the file, it’ll play it back normally. However, it won’t switch or make available a 5.1 audio track if it becomes available part way through a stream.
I’d also like to see this fixed 
Sad to hear that it’s not only a reporting issue but that it also doesn’t play the correct track either. I can see Plex possibly blaming a user’s ripped version for this issue, but where this is happening with their own DVR (still in beta) recordings, I would think this should be something that should be fixed as well.
Regarding your comment, “…snip the first bit of the ts file off (using dd or something similar).”, what is “dd”? Granted I can use Handbrake to take the beg/end off of a file (although it has to re-encode the entire video). I did look for something previously and found MP4Joiner/Splitter, but I and others have reported issues with the outputted file not playing past the first portion of the video (and it hasn’t been updated or fixed). My original purpose was to cut out the credits to join the post-credit scene to the end of the feature, rather than have them as two separate files. I figured splitting them and joining them together would work perfectly, but no dice.
dd is a program that simply copies files, or bits of files, on Unix-like platforms (so MacOS, Linux, etc). It can copy any type of file, but it has some useful features - you can easily use it to cut bits off the end of files or, like I do for .ts files, snip the first 100MB or so off a file if it’s got a 5.1 track later in the stream. You’re simply copying a portion of the video file (no re-encoding) so its a quick operation.
Using something like dd will only work on transport stream (.ts) video files, which Plex will save by default unless you use the re-encoding options. Those files are a copy of the DVB broadcast stream, and the broadcast stream doesn’t really have a start and end - transport streams are intended so that you can join it at any point and it will start playing. Using dd to snip the first 100MB off a transport stream file is like tuning into the broadcast stream 2 minutes later.
Most other video files (.mkv, .mp4) have a header which describes the content and length of the file. You can’t use dd to manipulate those files - if you snip the front off the file you’ll just remove the header and corrupt the file. If you concatenate files without updating the header, the player won’t know anything about the second file and only play the first file. As you note, Handbrake is the way to go with video files other than .ts files.
I haven’t used MP4Joiner/Splitter. It sounds like it should do what you’re expecting (update the header when you concatenate files) but I don’t know why it isn’t.
I have this too (point 3): https://forums.plex.tv/discussion/284669/shield-tv-and-plex-web-app-cannot-playback-this-recording-3-issues-found
I got a reply from @kinoCharlino so hopefully point 3 will be addressed, which will help you out.
point 3: Audio preceding the recorded movie (recording captured tail-end of another show because of 30 second leeway before movie starts) is 2.0, and Plex doesn’t switch to the 5.1 audio that the movie has: Watching with Kodi on shield (Plex for Kodi add-on), the audio output will switch from 2.0 to 5.1 happily and with correct framerate.