I don't particularly care for non-spec compliant MKV files. If you create such a file, its your own fault. There is only one proper way to mux H264 in MKV, and doing it another way will not only break this decoder, it'll probably output wrong timestamps with pretty much every decoder.
For H264 in AVI, at least there is only one way to do it, even if its ugly, and you can switch the processing mode on the file extension. But its not supported by LAV CUVID, and i have no plans to change that anytime soon.
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LAV Filters - open source ffmpeg based media splitter and decoders
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