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VFR Source.After encode,some frames remove,duplicated,remaining. Need help!

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Hi all,
i have 2 video, one is Source.avi (VFR, i think) and one is output.mkv (encoded by other one, not by me).
Everything in the output.mkv are fine. Audio and video sync.
But i dont understand why output.mkv has some frames removed, some frames duplicated, some frames remaining from Source.avi. It happened for whole movie.
I spent a lot of time to figure it out (try to read about vfr, decimate, tdecimate...) but no suceed. May be i dont clearly understand about these thing.
So you guys please help me, tell me how can they encode like this (from Source.avi to output.mkv with some frames remove, duplicate, remaining... and output.mkv still good). And give me an avs example.
I uploaded 2 videos here


https://www.dropbox.com/s/65x2yz6nyw4r1il/Source.avi
https://www.dropbox.com/s/dx7xdbycft5q0up/Output.mkv


P/S: Please take a note: the output.mkv is longer than source.avi about 314 frames at begining (they are credit of encoder, and i thing is not important in this case)


Thank you so much.

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