This is a mkvtoolnix support thread, not a MakeMKV or "playback on hardware players" support thread. Please create a new one for such a question.
One thing to look into: indexes (called "cues" in Matroska terms). mkvmerge always writes them, maybe makemkv doesn't or doesn't reference them from metaseek elements.
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Latest MKVToolNix is v83.0
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