I ran through tons of Apple and AE forum threads, searching for the solution. Ones said that it has something to do with CS5.5, others said that there’s a problem with the latest quicktime update version.
But in the end, nothing worked for me. This problem was featured with all the versions of AE I am using on my PC.
Oh.. and by the way I’m using Vista Ultimate on my main PC. And guess what.. this was the problem. The Vista! And it really has some unknown (for me) reasons not to run properly with the latest quicktime version, which is 7.7.1 by now. I’m saying that, because I have a laptop, where I’ve installed Windows 7 Home Premium. And that baby works fine with 7.7.1 making perfect renders in .mov format. Although, it’s a little bit slower comparing to my main PC, which is why it was a huge problem for me for a pretty long time.
Now the solution.
Just uninstall quicktime that you have right now. And look for the version 7.6.2. That’s it.