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Originally Posted by juGGaKNot
Hi'm wondering if i should let it use the fps it wants or override to the mkv FPS.
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Yes, override it to the correct FPS.
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Is this normal ? If not what should i use for mp4 and mkv to uncompressed video ?
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Obviously it is not normal. An option for you is DGDecNV which can decode MP4 and MKV and serve the frames via Avisynth. If you want to use VirtualDub for further encoding, you can open the Avisynth script in VirtualDub.