Not necessarily a solution, but see this thread:
http://www.kinodv.org/dcforum/dcforu..._id=2614&page=
If you have mplayer/mencoder installed, then it will be used in conjunction with ffmpeg. Otherwise, just ffmpeg is used. Therefore, if it plays in sync in mplayer (or ffplay if you do not have mplayer), then the conversion should keep sync. However, you might be affected by a bug mentioned in the above forum thread, and it contains a link to a new import script. You can save the downloaded script as ~/kino/import/media.sh.