System Stack seems to be the problem.
Are you running LibrePilot 15.09? If not, I would suggest upgrading to it.
If you are already running 15.09, then what about your setup do you think is even a little out of the ordinary?
You could export your uav file (so you can go back to it later), erase settings, and start over, and watch for what it is that you enable that causes the System Stack to be so small.