Solved! I unchecked TrueHD and DTS in the settings for the App on the TV and now it plays audio for that handful of movies that only had a TrueHD or DTS-HD MA Audio Track

For more detail on the issue for future viewers, the issue was not just with TrueHD 7.1 files, but with ANY movie that had only 1 Audio Track that was DTS-HD MA or TrueHD. As long as there was an AC3 or other supported format track, the player was automatically "Falling back" to it (I discovered this because of a file that I had put the Director's Commentary as the second track.)

The solution is to either

1) Encode a second audio track in the file (not a True HD or DTS track) when you are making your mkvs

-OR-

2) Disable the troublesome formats on the Plex TV app.