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For these sorts of problem, when I really care, I tend to encode a whole episode using the field matching or de-interlacing that mostly works, then I watch the encode and make a note of the problem sections. I'd re-encode them again, trying to fix the problems, and later split out the bad sections and replace them with the fixed versions. It can involve a bit of work... obviously... and it pays to always add --stitchable to the x264 command line if you want to append encoded video.
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