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Considering the history of MakeMKV's Matroska output sometimes being funky, it wouldn't surprise me if it had to do with mkvmerge having to fix the original mux in the first place. Eliminate that X factor entirely; use MakeMKV's Backup mode and then give mkvmerge the index.bdmv and do all the stream manipulation from there. That would confirm whether this really was a bug in mkvmerge or not.
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