A/V sync is one of the more difficult and annoying aspects of video conversion. You can't always rely on automatic converters to get it right when there are so many different combinations of codecs and formats floating around.
That's one reason why I usually do most of my conversions manually with ffmpeg or transcode or such, demultiplexing the audio and video so they can be processed separately, and only remuxing them back together at the end of the process. If I'm making a video dvd, I simply make sure the output is in
dvd-compatible mpeg2 format, which can then be used without major processing by most authoring programs. It takes more effort and knowledge of what you're doing, but it does give you more control and helps you avoid this kind of problem.
