Have you changed the overlay?
http://discuss.ardupilot.org/t/raspberry-pi-3-connecting-to-pixhawk/9524/10
http://discuss.ardupilot.org/t/connecting-raspberry-pi-to-pixhawk/9784
The docs should be updated for the rpi3
Have you changed the overlay?
http://discuss.ardupilot.org/t/raspberry-pi-3-connecting-to-pixhawk/9524/10
http://discuss.ardupilot.org/t/connecting-raspberry-pi-to-pixhawk/9784
The docs should be updated for the rpi3