I just installed the USS stepper board. I have been threading with the PP with no problems. With the SS board and the rpm exactly the same, 200 rpm, the z axis runs to slow and makes the pitch too fine.  Using the same gcode file for both with F=.039 in per rev.  With the PP it runs at about 8.5 ipm and with the SS it runs at about 7.8 ipm. Why is this happening? How to fix?

I would suggest asking on the warp9 website forum as that is better supported by the manufacturer