Spindle drives are essentially a Servo drive.

They need to know the orientation of the motor in relation to the encoder, so they know exactly how to power the motor, which is done orientation/phase sensing to learn the position of the rotor in relation to the encoder.

Typically the drive needs to know the encoder count, then go through the learning process to learn the motor.
Not doing this successfully results in what you're experiencing.

Unfortunately, that's as far as my knowledge on the subject goes, as I've never actually used an unmatched motor/drive.