I just got a new Samsung 55 in LED TV (UN55FH6003FXZA) and had the same issues as described in this thread in several places. I have a Gen 3 (1080p) Apple TV and I have a ton of Ripped Blu Ray's that I've used Handbreak to turn into Apple TV3 (preset) files. These play perfectly on my 1080p Mitsubishi Projector and my old 720p Plasma Flatscreen.
Once I got the new TV many of the video files started having small jerky parts that weren't horrible, but I did notice something wasn't correct right away. Then on one particular movie "Mavericks" it was unwatchable. The audio would play fine, but the video would get so hung up it would freeze and then try and catch up sometimes where it would speed up then freeze again..
I was also days from returning this TV and I tried this from an earlier post (below) and it's playing PERFECTLY now!!
Thanks Robemich!
robemich
I have a fantastic update for Samsung LED TV owners. You mileage may vary, but this worked for me.
Menu->Picture->Picture Mode->Movie
Menu->Picture->Picture Options->MPEG Noise Filter->Off
Menu->Picture->Picture Options->Auto Motion Plus->Clear
Not sure if the MPEG Noise Filter actually did anything or not, but this combination is working for me right now. I have no drops or jitter with Handbrake ripped content streaming through iTunes. SD or HD content both look great. Probably 95% of the content was ripped with AppleTV or AppleTV2 presets.
Hopefully this works for others out there. I was about an hour away from returning my TV for a Plasma.
-mike