I have a PIXHAWK running APM:Copter V3.5.1 Quad connected to the windows Mission Planner version 1.3.49 build 1.1.6410.20232 APM:Copter 3.5.1 and there are multiple problems with the Config Wizard.
The second compass is not working. I tried to use a different GPS/Compass but neither one makes a difference. I have both compasses selected but only compass #1 is working when calibrating.
2: When I get finished with all the configuration steps It asks if the drone can be armed but it also says the accelerometer config requires a reboot. I cannot arm the drone in this state and If I reboot, the com connection is broken and cannot be reconnected while in the wizard. The wizard is stuck in this mode and I need to use the windows task manager to stop the mission planner.
Finally, if I ignore the reboot and just try to tell it that it was armed ok, it does not save the configurations that I just completed. The same problem exists if I go through the mandatory hardware setup.
This all means I cannot configure my drone.