I am having a little hicup with setting the step motors, I fitted a UC400 and all seems to be working, I have always used it on mm's but since using pixelcnc I find it easier to design in inched, my brain does not understand what mm's looks like as it is wired in inches, so I altered the units in Mach3 to inches  when I was trying to get the step motors to travel the right distance,  I provisionally set the boxes on x and y to 320 200 200 I think I cant remember now. I used the auto tool ie asked x to travel 2" it travelled about 1/4" I then informed the programme of that when prompted, it then recommended a setting which i agreed to, tried it again and it was still not correct, tried to do this several times but it did not work, when I set everything back to metric and set the step motors to the original settings all was fine.
What am I missing?

It sounds like a steps-per-unit mismatch after switching from mm to inches. Try recalculating the steps per unit in Mach3 based on your leadscrew pitch and motor steps, then run the calibration again to see if the movement matches.