I believe this is a similar issue to (http://forums.plex.tv/discussion/285999) but it has not been resolved. I've got v6.15.2.4143 of the app. The issue has existed for a long time (since I believe the UI redesign and working directplay of 5.1 content).
What happens is that sections of video seem to have a stuttering effect that sort of makes them look like they're in slow motion. It only happens for a few seconds at a time, and is intermittent (i.e. play the same section two times in a row and it might happen or might not).
It seems to be related to a 24fps content. I've got a few test video sequences that I've transcoded from the source with a bunch of different options. 24fps content will exhibit the behavior. 30fps content will NOT exhibit the behavior.
I've tried encoding using 4.0, 4.1 and 5.1, but that doesn't seem to make any difference. 24fps content still stutters at any encoding level. 30fps content never does. (I also tried 23.976fps and 29.97fps but they behaved identically to their 24fps/30fps counterparts)
I've tried disabling the "match frame rate" option in the player. That seems to eliminate the stuttering, but introduced a new odd artifact where the video would stop for a frame or two every few seconds.
My TV (Vizio TV) has a "judder" setting. That seems to make a difference with "OFF" making the stuttering more frequent than "HIGH". I wouldn't stake my life on this one though. Maybe just placebo.
On the same TV I've got an old Plex for Vizio 3.13.13 client. It plays all combinations correctly without stutter and without server side transcoding. (it does transcode the audio to AAC in the server from DTS, but the video is direct stream).
My setup is FireTV -> Denon Receiver -> Vizio TV. All HDMI connections.
