www.makemkv.com

I have burned at least 10 blu ray discs, but only one has chapters on it. I use MakeMkv and then use Handbrake to encode the blu rays. The chapter markers are always checked and for the audio I use AAC avcodec for option 1 and DTS HD passthru for the second option. I then use Omgburn to burn the discs, but I can't figure out why I don't get chapters. American Psycho has chapters, but Iron Man 1, 2, 3, and Inside Man do not have chapters. What am I doing wrong?

Since neither Handbrake nor MakeMKV are intended as DVD or BD authoring tools, you really should ask the people who wrote your authoring tool this question...