Incorrect chapters

[grimmer]

I have been redoing several titles to upgrade from 480p to 1080p. When ripping these Blu-rays again, I noticed that the chapters are incorrect (as reported by Handbrake after scanning). I presume that the chapters are embedded into the MKV file and that is where they are incorrect (same number of chapters, but the actual time indexes make no sense and are out of chrological order). For an example see below (2 hour movie with 25 chapters, all less than 10 minutes). Is there a setting that I need to change? Or is it a bug?

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