David, The docs show 6 wires but you are right there are only 4. so I assumed the other two were ground and maybe that was a mistake. Looking at the rover from the pin side with top as top I connected the ground to the top set of pins on 1 and 3 and then connected 7,11 to the next two down on 1 and 13,15 to the next two on 3. I think I will remove the ground for now and see if that helps. Is it possible that connecting the top pins on 1 and 3 to ground may have caused the power problem that burned out the pixhawk? Something caused the APM power module to draw excess power through the pixhawk.
Tony
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