Actually, running Honor Pulldown Flags versus Force Film does not change the duration of the audio or video streams and so cannot change audio sync. However, choosing Ignore Pulldown Flags *can* affect the audio sync, and that is why you have to be very careful when using VirtualDubMod to decode MPEG2.
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After running a few encodes last night I have discovered that my original problem was the way in which I used (or didn't use) the Pulldown Flags for the audio.
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Audio does not have pulldown flags.