EDIT: This is in regards to the Navio2
Update: I went out to the same flight location today and flew. All things being the same, with the exception (major) of the 3DR GPS/compass addition. This external compass was enabled/calibrated and I had ZERO EKF errors of ANY type. I tried EKF1 and EKF2. They both worked fine. I used only the 3DR GPS and only the 3DR compass (disabled the two onboard compasses).
AM