I did an apt-get update && dist-upgrade command and it took about 15 minutes to complete. I’m wondering if I missed this step when I first installed the image.
Since upgrading the Bad Compass Health problem hadn’t come back in a day.
I’ve since removed the external compass and will give it a go with just the two internal compasses. Installed in an airplane this Navio2 is not surrounded by other electronics so the internal compasses should work fine.