I'm still confused about the audio delays. I demuxed Star Wars, added 1.017 seconds of silence at the beginning of the PCM track and compared it to the AC3 file. It matched perfectly. So I muxed the PCM track, AC3 track and my re-encoded video. But both PCM and AC3 were out of sync. I opened the d2v (DGIndex with forced film) file in virtualdub and selected the very first frame of the crawl. It started at 29.238 seconds. I opened the original PCM file and looked were the music for the crawl started. It started at 27.800 seconds. So I set a delay of 1.438 seconds and now the PCM track is perfectly in sync with the video although it differs from the original AC3 track.