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Any idea on the 3:2 aspect ratio issue?
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That just means that no ratio was used during the VFR-->CFR reencode and 1:1 is assumed. No big deal, as the aspect information is kept separately (720x480=3:2). Pseudo-BD structures are meant only as an in-between, and they also aren't very efficiently encoded (translated --> near-lossless and very big) to be quicker. But I can add the ratio information to the VFR-->CFR encode easy enough.
I'm going to look at the timecodes more closely to see where the anomalies are.