First mission item overwritten

Pixhawk
Firmware version: 3.3.3

I create a mission similar like a planned one in Mission Planner and transfer it to the copter via MAVLink.
The items are in order:
1: Takeoff
2: Do_Change_Speed
3: Condition_Yaw
4: Waypoint

The problem is, when I read this plan back from the copter to my software, the first command isn’t a takeoff anymore but a waypoint with all coordinates set to 0. In comparison, Mission Planner sets a waypoint (home) in front of the takeoff command, then this takeoff is the second command and won’t be overwritten… But this is nowhere documented. Is this behavior intended by the Pixhawk?

It’s also discussed here: https://groups.google.com/forum/#!topic/mavlink/SL0oTUJx1fE

Before, home was stored in position 0.