Problem Steps

I recently converted a 7x14 lathe, funds or lack there of has forced me to use the stock screws.
I'm using a automationtechnologiesinc.com 2 axis setup.

My Z axis seems to be working fine, the problem I'm seeing is on the X axis, which has a 1mm pitch screw.
I set up the stepper controller for the least number of steps, in this case 400 per rev, multiply that by 25.4 (I'm using inch mode) to get 10160 for my steps per

If I run a wizard and create the gcode for a facing cut, things come out close (off by .003)

If I change the jogging mode so I can step at .001 and use a test indicator(mitutoyo) it only steps .0005-ish

If I double the steps per setting it then steps .001 but when I run a program it's way off .2 or more

another fun thing is the backlash settings, If I set it at .001" the motor spins but it doesn't start moving, if I put it to .002" it jumps .005"! :eek:

writing it down starts to make me think it might be a stepper driver issue, but they seem to work other wise - I'll try changing the step settings maybe that will help.

any ideas or suggestions would be greatly appreciated