Ok, I know than little PTS differences in subs aren't important. We can forget that.
My test with my second BD work fine, all is the same using iso or mkv, with the know differences in sup's and chapters.
I'm check the chapters differences, and qpfile generated, and I see:
Code:
Time Time Time I-fra. I-fra I
Chapters Bad from mkv Ok from mpls Dif. mkv QP mpl QP Dif
--------- ------------ ------------ ---- ------ ------ ---
CHAPTER01 00:00:00.000 00:00:00.000 0
CHAPTER02 00:06:08.618 00:06:08.785 -167 8838 8842 - 4
CHAPTER03 00:12:20.406 00:12:20.490 - 84 17752 17754 - 2
CHAPTER04 00:17:30.591 00:17:30.591 0 25189 25189 0
CHAPTER05 00:23:51.054 00:23:51.180 -126 34311 34314 - 3
CHAPTER06 00:31:26.509 00:31:26.676 -167 45231 45235 - 4
CHAPTER07 00:35:54.485 00:35:54.486 - 1 51656 51656 0
CHAPTER08 00:42:29.421 00:42:29.547 -126 61125 61128 - 3
CHAPTER09 00:47:03.362 00:47:03.612 -250 67693 67699 - 6
CHAPTER10 00:53:16.318 00:53:16.318 0 76635 76635 0
CHAPTER11 00:59:12.632 00:59:12.716 - 84 85178 85180 - 2
CHAPTER12 01:04:38.040 01:04:38.041 - 1 92980 92980 0
CHAPTER13 01:08:32.108 01:08:32.108 0 98592 98592 0
CHAPTER14 01:14:22.416 01:14:22.416 0 106991 106991 0
CHAPTER15 01:21:03.483 01:21:03.609 -126 116607 116610 - 3
CHAPTER16 01:25:42.011 01:25:42.012 - 1 123285 123285 0
CHAPTER17 01:36:08.679 01:36:08.680 - 1 138310 138310 0
CHAPTER18 01:41:29.333 01:41:29.625 -292 145998 146005 - 7
Like I can't understand for what the differences I checked the I frames in video (must be the sames in mkv and mpls) and I discover than the I frames calculated with the mpls aren't always I frames in the video, but all calculated with the mkv chapters are I frames in video.
Then seems than MakeMKV correct chapters times to point real I frames in video, and the qpfile is better because point to real scene changes.