If you look through the topic posts you’ll see there were two different issues - I summarize them here.
Essentially - you have an AC3 in MKV bug which is a Roku issue introduced in 9.4 and there was a transcoding 5.1/7.1 to MP3 bug which Plex has fixed in recent Roku app update.
By turning off Direct Play on your Plex app on Roku you can get around the AC3 bug until Roku fixes it and updating your app you will fix the 5.1/7.1->MP3 transcoding bug. This should avoid having to do any conversions.