Hi Dragan
I have just found your thread, am having the same problem with a hi sped machine and cs5.5.
Have you had any joy with your issue and perhaps solved it?
The only thing different that I can see is that if I do a mp4 render and then use media encoder to output that mp4 as a mpeg2 it seems to fix the problem, but I am not convinced or have faith in CS5.5 too much at the moment, that it will not fail again with some choppy scenes.
Interestingly, the mp4 when played back has a choppy section at the beginning but the mpeg2 from it seems fine.
Glen