Problems rendering from CS6 using H.264

I'm trying to render out an H.264 from CS6, but getting really glitchy grey pixelated results. So far what I've diagnosed is that if I render from CS6 using format H.264 I get the issue, but if I render out as format Quicktime using the H.264 codec the movie is fine. I tried rendering out in CS5.5 and in both cases there are no problems, which makes me think it's something to do with the way that CS6 handles the H.264 format.

Here is the version from AE CS6:

..and here the same file rendered from AE CS5.5

One other thing to note is that the problem doesn't seem to show up when viewed in Quicktime 7.

I'm on a 12 core MacPro running OSX 10.6.8 and have AE CS6 11.0.1.12

Any help would be appreciated.