Remote control autopilot stops responding.

I'm using autopilot to perform some maneuvers after disconnecting from a connector. The problem is all thrusters stop working and the ship just points in the direction of the way point it's suppose to go to. To fix it i just have to get into the cockpit and move a little and the remote control will kick in and take over. I need a programmatic solution though.

Thus far i have tried:

Overriding thrust - does nothing as I've said, the thrusters stop working
spinning the ship
waiting for a few...

Remote control autopilot stops responding.