Plex Windows App Stuttering on playing some mkv video

I've looked through the forums and haven't seen anyone else complain about this but since around November I've noticed the PLEX player for Windows stutters and pauses on certain files (seems to be some mkv's while not others)
Using the Plex in chrome works fine with the same file , of note these files are direct play and not transcoded.
Using mediainfo to try to figure out what the problem could be has been non conclusive as there doesn't seem to be a common codec in the container I can point to.
I'm surprised nobody else has reported this, it's happening on my surface pro 3 as well as the my tower 6700K/ amd R290X full PC so it's not a processor issue it's something with the 'Universal' part of Windows and playback in Plex since it's not affecting Chrome/Firefox.
Has anyone noticed or looking into this?