This can happen if you're rotating your thrusters and they are under load, especially in gravity. This will also happen if you're using multiple thrusters on a rotor. The way the script works is that it's possible that different thrusters will have different override settings. If one thruster is unbalanced in relationship to the rotation of the rotor, it becomes a lever. If the amount of force is greater than what the rotor brake can handle, the rotor will slip until it catches the max or min limit (if being used).

I've found that rotating a thruster is easier if that thruster is off and not creating torque. Setting your inertial dampeners off and not thrusting will also work.