The issue is not resolved. It will require a software update to fix it. Hopefully it can be fixed.
It's not related to any specific material. I watched a movie I purchased from iTunes tonight (Sky High in HD) and saw it numerous times. Yes this streamed from my mac pro to my new apple tv, but a) the buffer completely filled up and b) streaming the same movie to my old apple tv does not exhibit the problem.
Initially I reported that it was happening every few seconds. On this program I saw it less often, more like every few minutes, with a bad one every 10 minutes or so. Sometimes it's hard to see, only a single frame skip or dropped frame. So if you're not watching for it you might miss it. To me it completely takes me out of the movie and makes me aware that something is wrong. Like a kid crying in a movie theatre.. or like when I saw Star Trek and there was a cluster of burnt pixels in the middle of the screen. For a videophile it ruins the movie.
There is a discussion over at mac rumors that has more information. Check that out to see some of my experiments trying to figure it out. I have yet to read all 6 pages here but am about to. If you see it please report it to apple using the link on this thread.
http://forums.macrumors.com/showthread.php?t=1034558