I have the same problem. I found a couple of things out today.
1. This problem does not seem to be happening on TVs that are 720p. I know this, because I have a 720p tv in my bedroom and all the shows and movies work great. Most of the time. I have had issues with MadMen a couple of times, but only on one episode in the 4th season.
2. It seems to be only the HD shows and movies that are affected, but not all of them.
I tried Michael Allbitton's suggestions and I watched SGU successfully, however, when I tried to watch Walking Dead series, I failed miserably.
I also tried to watch How The Universe Works and Steven Hawking's Universe. When I tried the latter two, at first, I had no sound. I power cycled my tv and lo and behold, I had sound. I did try it on WD and Caprica and some HD movies as well and it was not successful.
I have tried new HDMI cables and had my ATV replaced yesterday, to determine where the problem lies. It's NETFLIX. Though I doubt they will ever admit, that it's their issue, I firmly believe this is the case. THey need to at least address that it "could" be an issue and try to troubleshoot the problem, rather than just pawn it off on Apple and say there's no way it could be them.
I hope they fix it soon or another company finds a solution. I would gladly switch to a service that works, than deal with this for the next however many years to come.
If I discover a solution, I will gladly post it here in the future.