I have been using RasPlex 0.4.0-rc4 for a while and it has worked flawlessly, I think I was using Plex Media Server Version 0.9.8.10. I recently upgraded to Version 0.9.9.14 and started experiencing playback issues especially on HD content, stuttering and buffering mainly to the point where things were unwatchable.
After some digging around I found there is no a file called Plex Home Theater-RaspberryPi.xml file in the Plex Media Server\Resources\Profiles Folder (this wasn't there previously, I checked by installing the old version of PMS on another PC). Once I changed the file extension to .old so that it wasn't referenced every started working as normal again.
Not sure if anyone else has had issue with this. Just thought I would post it in case it helps anyone out.