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Well I can replicate it.
Basically HT profiles don't allow qpel, GMC or quants other than H.263. Also if bframes are enabled, they are limited to 1 consecutive with pb enabled. I also made sure that N-VOP's don't get used and from recollection, if interlacing is enabled, bframes are disabled.
You can check my theory by disabling bframes. Should result in an encode without bframes. This would not be the case if the settings were simply being ignored.
I should have time tonight to have a proper look and hopefully fix it.
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