I have a Pixhawk on a 3DR DIY Kit Quad and it flies well in all autonomous regimes except:
It will not automatically land after a mission if there is a land command in the mission. I have to click "land" on mission planner for it to do so.
It will take-off but then just hover at the take-off height and fail to proceed with the mission. I have to go into stabilize then back into auto for it to continue the mission.
(Data flash will be up soon, don't have access to it right now)