I was using a clean install (default settings) in tsmuxergui. So when you get to the video portion of the 2nd disc and hit your chapter forward it goes to the end of the movie?
Strange. Mine has 49 chapters if I recall properly.
I didn't get that far because I stopped when I noticed the chapters list in the Blu-ray tab were wrong. That's when I decided to go ahead and calculate the chapters on my own.