mjuliaoi, I just tried Dr DivX the other day and noticed the same thing. While I did notice good video results, the audio was skipping and also was not in synch. I haven't had time to research it out yet. Perhaps someone else knows a fix or workaround for the audio problem with Dr DivX... p.s.: This app shows some promise but I wish they wouldn't have released it with all the "known issues," did you read the readme?!
I'm not sure what might be causing your audio to go out of sync. But you can go to the official Dr. Dvix Forum and check out what other Dr. Divx users have or if they have come up with the solution. Here is thwe Addy. http://forums.divx.com/viewforum.php?forum=24