NAVIO2 - Inconsistent Compass Problems

As long as you are using the most recent ardupilot builds I don’t think you’ll need to roll the second compass, its compiled in when compiling for the Navio2 board. ardupilot/libraries/AP_Compass/AP_Compass_LSM9DS1.cpp at master · ArduPilot/ardupilot · GitHub

I ran into the same problem but mine was really bad EMI, external compass fixed my inssue, but some good info here.