As suggested I erased the eeprom and got almost the same values. Have now installed 3.5-RC1 did a compass calibration and got vastly different readings and compass 3 has disappeared now I am confused!
Best way to clear the EEPROM is to load Rover, then Copter (please check if this is true for PX2.0 first), but that’s just a long shot.
On my Pixhawk (classic one), I have disabled the internal compass, as its too close to the ESCs and I get similar readings (though 7xx readings is WAY WAY to high, seems like HW failure).
Normal thing to do next is a compass-mot and disable compass #2 and #3; give it a test flight. PX2.0 should be more advanced, and I really wouldn’t get the point of having other compasses disabled though.
I never read if you tested the board AWAY from any electronics (I know its just powered by the USB), but you need to isolate the issue. Lay it flat on your desk and plug it in. Anything in your room causing the error? Maybe the desk? (just brainstorming).
Have you flown that board before? You might be looking at a defective one and start trying to contact the vendor or 3DR.