Neale, I have exactly the same problem, did you manage to resolve it?

I don't have stiffness problems on the machine, to test I am only cutting 3mm deep slots 1mm at a time, i have tried 0.5mm at a time.
I have set the steps in mach3 and can run the machine up and down the x and y axis all day at 3m/min and still go accurately back to the start point.
Not losing steps have dial gauges set on the x and y axis at the home, so i would see and changes.
I have measured the bits and they are spot on.
I am using aspire to generate the gcode

I have also setup Uccnc to see if its a Mach3 problem, still the same

2005mm ballscrews (not out of align)

I have tried cutting a few lines 25mm, 50mm, 75mm long using profile cut and 100mm, 50mm and 25mm square using pocket cut, all out by 0.2mm to 0.4mm

I tried 4 slots (for a guitar fretboard) that should have been
35.64 measured 35.98
33.64 33.86
31.75 32.00


Any ideas?