Atak,
So I converted 3 movies and the audio sync is fine. So I decided to convert MI2 (Mission Impossible 2 - the file that gave me the problem) and I have the same issue (audio out of sync). Here is a link to an an excerpt of the video.
MI2
Not sure what to do. I had the same issue with MI3. Tomorrow I will try that movie again.
Thanks for the demux question!!