Servo motors ..no microstepping set it to one ( 1)
If Your shaft encoder generates 1000 pulses per revolution and it outputs a quadrature signal then Your driver ought to be able to resolve 4000 distinct points around the circle.
I guess You are using step/direction to drive the servo then it is equivalent to a stepper with 4000 steps per rev. I think You are using an encoder with 250 pulses in quadrature, treat it like a stepper with 1000 steps per rev.


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Note to self. Always look what forum you are in before opening your mouth. (I was using the search engine to locate information and stumbled in on this post) 