In cases like that, I always extract the audio and remix them later. If your video encoder doesn't do that, you'll need to find one that does.
I am trying to convert a 2 ? hour musical that is in WMV PAL format to NTSC DVD.
I used ULEAD Movie Factory, to create to DVD, Blaze Media Pro to convert to MPEG2 NTSC. My problem is the same, especially in the last hour the sound is badly out of sync from the picture. Any help is much appreciated.