It happens because tsMuxeR uses different base IN_TIME (00:00:11.650 or something like this, I can't remember). Chapters set in mpls files and fine/coarse tables in clpi files are based on it... in other words, all packets in the remuxed m2ts carry different PTS stamps compared to the original m2ts file... That's why I find it strange that it even works if one keeps the original clpi+mpls files.
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