@mkver, wow, that's a complicated story!
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This means that this stream is simply out-of-spec!
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That might explain why tsMuxer totally tripped on it (badly broken and jittery output). I was able to extract the main stream correctly with eac3to.
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But it also has ct_type equal to 1 which means that the original source material is interlaced;
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There's some visual evidence for that too; darn if I can find one now, but earlier, I saw a few frames with your typical interlaced 'stripes' artifacts in them (as if badly deinterlaced). It's this way on the original .m2ts blu-ray too (so it's not an eac3to extract thing).