Zero thrust in transition from POSITION to MISSION mode

Hello there,
I have been flying a quadrotor with mRo pixhawk 2.4.6 and FMUv3. Sometimes during transition from position to mission mode the thrust passed for motors reachs zero value causing the drone to lose altitude suddenly as can be seen in log and figure bellow.

It never happens in transitions between other modes.
I would appreciate any help on this issue.