OK, thanks for the tests.
If I understand correctly, the chapters in the MKV are different than in the original BD, but they are better because they are perfectly aligned with the I-frames. Right?
For me, it's not necessarily a good point, because BD3D2MK3D creates an I-frame at the chapter point anyway (with the qpfile), but indeed, it MakeMKV sets it to a real scene change (which coincides with an I-frame almost always), it's good. It's less good if it chooses the I-frame immediately before or after the scene change.
Anyway, I have no way to modify the chapters myself. I can only trust the chapters in the MKV. I will just verify if the chapter timings are identical with all programs (tsMuxeR, eac3to, MkvMerge, MkvInfo and MediaInfo).
I may release the official v0.87 in a couple of days, if no new bugs are reported...
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