Here's how the shock works.
The shaft can turn 90 degrees. So it has two built in stops.
0 degrees and 90 degrees.
When you turn the shaft on the shock absorber, its position will control the dampening effect of the shock absorber.
When you turn the ignition on, the FX3 does a self test and the actuator positions the shaft of the shock in a know position.
The actuator is a motor that can turn either CW or CCW and has a feedback signal so the FX3 control module can monitor the speed of the motor and its travel direction.
So when you first turn the ignition on, the actuator turns the shock shaft one way until it hits the stop and then the other way until it hits the other stop.
For example. If the shaft was frozen, the motor would not move. There would be no feedback signal from the actuator. The FX3 control module would set the code that the actuator didn't complete its task in the proper time.
(Time out).
During the self test, the FX3 control module also expects within a certain time frame the actuator should hit the stop either in the CW or CWW direction. (The shaft turns 90 degrees, you manually verified that). So if the actuator motor just continues to run and no stop is found you would get a (Out of position). The Control Module has no idea of the position of the shaft.
The manual says to remove the actuator.
You manually moved the shaft and it did rotate 90 degrees with little resistance. This indicates the shock is good.
Did you verify the gear on the shaft of the shock is good?
The manual says to turn the ignition on and you should see the inside gear of the actuator move in both directions.
If the motor moves in both directs, the manual says to check the voltages on the plug that goes back to the FX3 control module. If the voltages are correct, replace the actuator.
Most problems are the gear on the shock is stripped or the gear inside the actuator is broken.
For test purposes if this is a front shock, you could clear the codes and swap the actuator from one side of the car to the other.
Also when I said you can just snap the actuator back on, you do have to verify the wiring harness is properly positioned so it doesn't get damaged.