Hey there, at some point i had the same problem as you, my solution is not really a very smart one but its the only one i could find, unfortunately i downgraded to CS3 and everything works fine after you update it and install Mainconcept mpg pro HD, maybe you can try installing this last plugin and see what happens, as a said, I know downgrading the soft is a stupid way to solve the problem but film and editing is what i do for a living and I really cant stop working for a week until i find a real solution. I also use a Sony FX1 and i had some trouble with renders such as black frames or frames coming out of place for a second in CS4, none of this seems to happen in CS3, so i dont really know what is causing the problem, all i can do is guess. I hope this helps with your problem.
Gabriel