In Makemkv are you keeping it simple and just selecting one audio track and no subtitles and Handbrake's is still crashing? I've had some problems with handbrake when I don't deselect everything except for the main Audio/video track.
Yes. I have tried re-ripping with makemkv as well. Unless I know the movie has forced subtitles, I always only select video and audio. Everything else goes unchecked.
As I suspect there are actually three different video files (according to bdinfo) Two are identical streams for the main movie (stream 950 gets excluded by makemkv) and the other is the bluray live version. I also have now tried using tsmuxer through windows and exporting both .ts and .mpts in Handbrake. Handbrake crashes on both. also at the same timeframe in the encode (about half-way through at what would be chapter 12).