I was able to reproduce your problem. As it turned out, even though 3.0.1
was a minor release for other boards, Navio 2 was affected drastically. For the time being you can download the latest stable from here.
wget http://firmware.ardupilot.org/Rover/stable/navio2/APMrover2.elf
chmod +x APMrover2.elf
- Remove old params and launch
- Perform onboard calibration (this does work now on both compasses!)
Thanks a lot for reporting. I’ll try to upload the newer debian package with the proper version by the end of this week.