i've been having a problem when I encode .avi to DVD, sometimes the ac3 file is shorter than the video. I understand there may be some corruption in the avi and maybe it's keeping it from encoding the rest of the audio.
is it possible to set it to keep encoding the whole length of the movie anyway?
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Are you using "DVD ffmpeg"? If yes try to enable "Decode with Quicktime" so as video and audio will be encoded separately.
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