I think using eac3to (Haali muxer) to auto remux in mkv is very outdated and it's the culprit of such issues. Check here:
https://github.com/HomeOfAviSynthPlusEvolution/L-SMASH-Works/issues/43
Cause Megui auto remux chapter in Bluray source, I can't change it to use mkvtoolnix (mkvmerge) so I need you to edit to use mkvtoolnix (mkvmerge) replace eac3to (Haali muxer) in auto remux