If the recalibration of the joystick is not finishing it would indicate an issue with the joystick - but this error can also be caused by something holding the joystick out of the zero position on start up.
So if you ensure there is nothing touching the joystick and then restart the controller it should start up without error - if this was the cause.
The joystick is available as a spare part, the spare part number is 3HAC028357-026.
i am having a similiar Problem and i am currently wondering how you got into the joystick calibration menue.
I can not find anything in the manual, and on the FlexPendant itself i can only find the touchscreen calibration. In another thread i heard something about a combination of joystick moves, but i am not sure if that applies for this model.
it would be really nice if you could tell me how to enter the joystick calibration menue!