As far as the update for recompressor it was an ffmpeg profile update only. The profile had gotten corrupted somehow. So the add stereo and dolby digital weren't working completely correctly.
So the basic concept is you need Plex to play directly. Anytime plex changes it for whatever reason, audio subtitle, you name it, it will then transcode it with ffmpeg which will add the colour info back in. Which is fine if the Roku would handle it properly, but obviously that is not the case.
For me I set the option Force Direct in Plex. If you don't have a compatible audio channel you will get no sound. Doing this makes Plex NEVER transcode.
When I rip a movie I always add stereo and dd 5.1 and that profile also strips colour header. And I have no issues anymore. What the profile does is grabs the first audio and makes a dd 5.1 and stereo stream in the mkv.
For this example, it's an old movie and already has ac3, So I just need to add stereo. You can see the mapping in the log...