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Originally Posted by nm
They use the lavf MP4 muxer, which works just fine AFAIK. The problem seems to be in MEncoder and its b-frame handling.
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Which means the same muxer as mencoder. And the latter failed on me with the only x264 option specified being crf, which means zero b frames. Maybe it's mencoder, but frankly it'd surprise me.
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Never had a problem with it for these purposes and this seems to be what most people are now using it for. Personally I prefer MEncoder, but that's because I already know the tricks to make it work.
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Thanks for the feedback. In the meantime, I checked again and found once more that avidemux is not really what I want, effectively being too gui bound. The quest continues.