I have a matek h743 mounted in roll 180 and a matek m8q-5883 gps compass monted flat, so i have the option ahrs orientation in roll 180, but i am having a lot of ekf status warning in compass. so maybe i have to set the compass orientation in roll 180 or i dont know what can be causing problems.
you are able to change orientation of both. have you calibrated your compasses and what does the compass page show under setup?
Advanced Compass Setup — Copter documentation