I'm having trouble calibrating my compass on my quadcopter. I'm using an external GPS/compass that I got from China (not 3DR brand). It's attached via a mast to a Pixhawk clone, which I think has the newest firmware (I just updated it on Sunday). I performed the compass calibration in MP, selecting the Pixhawk option and saying that I'm using firmware AC 3.3. When I do the calibration, the offests I get are gigantic - up in the 2000s and 2500s. On the Flight Data page of MP, the copter always seems to know which direction it's pointed. But, since the offsets are way high, it doesn't want to arm (unless I turn off that particular prearm check), and I get lots of failsafe alarms when I'm flying, due to what I think is the EKF / DCM Check & Failsafe.
Can anyone help me figure out why I'm having such trouble? The compass is on a mast, and it won't get a good calibration even when away from as much metal as possible.