The video has been recorded upside-down but a flag in the MP4 container tells players to rotate the video by 180° upon display (so that display is corrected). When mkvtoolnix remuxes the mp4 file this flag is lost because such a flag doesn't exist for mkv. Nothing you can do except re-encode the video or stick to mp4. (There are SEI messages for orientation in H.264 that mkvtoolnix would keep but I don't know a software to change them nor if any player supports them.)
Last edited by sneaker_ger; 19th July 2018 at 22:08.
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