@Wieland, Can you give more details?
What OS are you using? Window / OS?, what are you using for telemetry comms? RFD900? / 3DR radios? In your other post you say you have tried MP, AMP2 , and QGround Control? What versions/builds?
Have you followed the joystick/gamepad wiki?
I am using Pixhawk Rover with latest build ( v3.0.1), MP latest build (1.3.41 build 1.1.6110.31287). I can connect the MP to the Pixhawk, telemetry is accurate and functions, I can open the Joystick settings window and change the settings, mapping the rudder and throttle, also mapping/setting the mode change buttons. As soon as I hit enable the output bars freeze and the joystick does not engage with the boat. Once I disable the Joystick the output bars become responsive to the Joystick.
The other point to note is that MP does not save the joystick settings. If I close the joystick window and reopen or close MP and reboot MP all of the joystick settings as lost.
So if you are having the same problem with Arduplane and I am using Ardurover this could be a problem with MP but as you are using other GCS’s this is confusing.
Possibly the preflight checks failed.
Please check the messages tab in your APM planner soft.
Some of them can be disabled, at least for testing purposes: http://ardupilot.org/copter/docs/prearm_safety_check.html
After that, clicking the ARM button on the Actions tab should work.
After that shaking the drone should initiate the motor propeller.