I'm have trouble getting the Z axis to move the specified distance. When instructed to move 1 inch it moves .77 of an inch. I have tried a bunch of difference setting in PncConf Wizard and just can get it to come out right. I even tried setting it up as if the Z screw was a .2 inch screw rather that the metric 5mm screw that the kit was supposed to come with. I don't think it an issue with losing steps because the measurement is the same moving the Z up or down and it is consistent. I have the head counter weighted.
I'm converting a Sieg X3 mill using the CNCFusion deluxe kit, Mesa 6i25 + &i76 Plug-N-Go kit with a Gecko 203v driver with 10 micro steps on the Z axis. The ball screw has 5mm pitch. I'm having no problem with the X or Y. They are using KL-5056 drivers set to 8 micro steps.
Someone on the LinuxCNC form said something that made me remember that there were pulleys on the Z and they weren't 1:1. That motor is under a cover and I was so focused of t he software set I forgot about the pulleys.
Measure how much the block moves for one rotation and enter tpi value in "axis scale calculation" and enter "microstep multiplication factor" too.
Hope that helps.
I solved it a while back. I forgot that the Z went through pulleys that were not 1:1 because the Z motor was on the back of the mill under a cover. Out of sight out of mind.