Unexpected behavior when using takeoff command


We got some unexpected behavior when using takeoff command in Guided Mode. The drone suddently do some kind of repositionning without input leading to some ramp ouput on roll or pitch.
It generally append when APM: EKF2 IMU0 in-flight yaw alignment complete
APM: EKF2 IMU1 in-flight yaw alignment complete is received
I suspect some error when transitionning from the end of the takeoff controler and normal controler.
Here is a video of the bug and a log. https://drive.google.com/open?id=0B_NEM1LjTY6pTGdyaURXajBHdGs

The version is based on 3.5.3 with correction on NavGuided handling for auto and new switch option to select between Rc_override and RC remote (PRs comming soon) so nothing touching to controlers.
The board is a pixhawk 2.1.