I am trying to rip a 2 disc blu-ray to mkv. Handbrake worked fine for the main disc but for the extras disc it doesnt seem to pick up anything substantial. All the chapters are just a few seconds long when they should be like 20 min on average. What alternatives are there for ripping Blu-Rays? I tried K9Copy on the stream folder but claimed it could not read it.

don't think there are a lot of alternatives, have you tried makemkv http://www.makemkv.com/forum2/viewtopic.php?f=3&t=224

have you asked on the handbrake forum https://forum.handbrake.fr/ about extras disc?