Since the XB1 MKV support is currently requiring transcoding, I have been considering remuxing my content over to other containers to allow for more direct play/stream.
It occurred to me, since the content of those containers is the same, wouldn't it be relatively easy for the Plex server to remux on the fly? That would have to be less intensive than transcoding, and would gain the directplay/stream benefits for out MKV libraries?
Check [this](https://forums.plex.tv/topic/147277-bluray-1080p-rips-vs-dvd-480p/) thread, maybe you are running into something similar.
Basically in my case in that thread, for some reason when the anamorphic flag is set and streamed to the Xbox One client it transcodes instead of "direct stream" which is when it is just remuxing. If you remux to an mp4 container with the same audio/video streams it will direct play. Hopefully something that the devs will look into.
Also, make sure the bitrate of your source file is less than 20MBps. Anything higher and the video will be transcoded regardless of any other settings.