I have the same problem all the time with Nero as well....
The only solution I came up with was to convert the file with Super and then place it in Nero Vision, it then goes through the transcoding stage again, but for some reason this was the only way I could get that movie onto DVD and have the audio in sync with the movie...
It's a long process, but the only solution I have found....
Link to Super....
http://www.erightsoft.net/Superdc.html