"some other clues: It rarely affects the Z axis mags so perhaps the i2c busses are working normally. It will happen when powering only from USB only so it's not interference from the ESC and motors."
i'm having the worst trouble with mags on the HK Pilot pixhawk clone. All mags are throwing wacky values near 65535 and then snapping back into normal readings. You can see the spikes in the graph below. These spikes cause flipping crashes when…