Mpeg2avi audio delay issue

[Brand X Media]

Okay here's the deal, I am working on a GUI for mpeg2avi which will allow drag n dropping of files and auto bitrate adjustment given the film length. My problems are as follows: If I take a VOB other than the first one in the stream and encode it separately my audio is in perfect sync (using an AC-3 track). Once I try to encode the first Vob there is a 1 second delay of audio. I am having mpeg2avi demux audio. I am all but ready to give up on mpeg2avi despite the nice quality, because again in trying to make a stand alone answer to encoding, I would rather not use Nandub in efforts to match the audio track after having spent 2 1/2 hours compressing. Any answers as to why this happens or how I can remedy this?