HI @uncletim ,
Yeah, neither of the examples you posted are Direct Playing, so you will still have the red for sure. When the server Direct Streams, it copies the tracks to a new MKV container, and restores the color info in the header. So the red comes back.
The AAC one is easy to understand. The AAC 3.0 track can't be directly played on the Roku. You need to transcode it to AC3 or downmix it to AAC 2.0 to get that one to play correctly. Remember that in MKV files it is perfectly permissible to have mutliple sound tracks, so you don't have to throw your AAC 3.0 away.
The DTS one is a little harder since both tracks are evidently compatible with your playback equipment, but the server has decided to Direct Stream anyway. You should double check to make sure Direct Play is enabled on your Roku. You might even try to force it to Direct Play. I would also try adding an AC3 track to see if that helps the server think it is OK to Direct play it.