Hi Clem,
Rather than tuning the EKF, it’s usually best to find out exactly what’s upsetting it in the first place.
Both your logs have the following entries just after take-off
EKF2 IMU0 ground mag anomaly, yaw re-aligned
EKF2 IMU1 ground mag anomaly, yaw re-aligned
Seems other people experienced similar issues:
http://discuss.ardupilot.org/t/ekf-ground-mag-anomaly-has-anyone-heard-of-it/15665
and more here…
http://discuss.ardupilot.org/t/nightmare-compass-calibration-solved/15421
I can’t really tell exactly what is happening, but if this was my rig I’d have the compasses as my prime suspects.
Justin