Gotta say, I'm not having much luck with Plex at this point. To me, the whole point is to have an app that will play the h.264 BR rips I have on an HDD connected to my AEBS and let Plex do the audio transcode. I have tried LOTR-EE and it plays horribly, stuttering and buffering with slight video tearing artifacts. MY AEBS and media server are in the same room as the aTV and wifi signal is strong.
It plays my Handbrake transcoded mp4's fine but then, the only thing Plex provides over iTunes is a pretty interface, nice to have but what I am looking for is something that can play the uncompressed BR rips.
Edit: I should add that the mkv's I trying to play have DTS audio, so Plex is still having to transcode the audio.