Frameskipping and Samsung TVs
I see this thread is kind of dead, but I think I can throw a little bit of light to the frameskipping issue on the Apple TV 2G.
I had the same issues as described, either with movie trailers or with purchased HD movies. I also ripped a .mkv to .m4v to see if the problems were the same, and no good news either.
I tried the ATV on another TV (small 19" LG) and I had NO PROBLEMS AT ALL on that one. So, googling around I found this other guys referencing a problem with HDMI signal drops with Apple TV 1st gen and Samsung TVs. I know it is not related to this issue but I thought 'what the heck' and gave it a try:
http://hints.macworld.com/article.php?story=20081207011101698
My problems disappeared... for a while. When I did what's mentioned on that post, I noticed that all the settings I had on my HDMI inputs (Dynamic contrast, DNIe, Movie stuff and so on) had been reset to defaults.
So, I started playing with the settings of the HDMI input. I still cannot tell which setting did what, but I can guarantee that the frameskipping totally depends on those settings. I have it now working like a charm. No frameskipping, no 'slowdowns'... If needed, I can post my settings of the input, but it will surelly depend on the TV model.
Apple definatelly has issues, at least, with Samsung TVs (mine is an LCD Series 6) but I think there's a little workaround by now until we get a firmware update.
Hope it helps. Please, let me know your results with this if you try any settings of the HDMI input where your ATV is connected.