Hi Nige,
I got your PM. Here is how you do the math. I will give you mine as an example. What we need to know is, How many pulses from Mach will it take to move the machine 1 of your units? (inch,mm) Mine is in inches. 1 inch = 10,000 pulses on mine. This is how I came up with the number.
My steppers have 200 pulses per revolution. ( 360 degrees divided by 1.8 degrees = 200 )
Micro stepping = 10. So 200 X 10=2,000
Motor to screw gearing is 1-1. So 2,000 X 1=2,000
Screw lead is .200 of an inch. My screw will have to turn 5 rounds to move the nut 1". 1.0 divided by 0.200=5. So 2,000 X 5=10,000.
Do the math first. Then we can move on. Once we are certain of all of this, dialing it in should be easy. Right now we don't know if you are skipping steps because the accel. and vel. are set to high or what.