In the past I've used a command line program called xport to demux the video and audio from the transport stream. It cuts the beginning of the audio to sync with the video so there is no need to apply a delay.
What was your solution?
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I found a program called "DelayCut", which cuts the delay off the audio file. You just have to know what the excat delay value is, but that's written into the filename that DGIndex put out.
Then I loaded the AVI script (with only the telecide and decimate commands) and the audio file into DVD Flick, which did the rest ... resizing, remuxing, authoring. I am now adding chapters with TMPGEnc.
The only strange thing left now is that there should be very thin black bars above and below the picture. But there is no black bar above the picture, instead there is a black bar double the normal size below the picture. It's only visible on TV, not on PC. But that's a very minor problem that probably nobody will notice.
Everything worked out fine, finally! But I never could have done it without your help! So, if there is anything I can do for you ... maybe a copy of the movie in question?
Time is the fire in which we burn