Seems the FFMS2 + MotionProtectedFPS combination doesn't like it when the frame serving is not consecutive.
The HCenc predictive phase uses samples of 3 consecutive frames, with variable frame rate it seems to be hard to locate the next 3-frame sample in the source.
Better to use a regular 2 pass encode in these cases.
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HCenc at: http://hank315.nl
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