Check what your actual stepper drivers rev (microsteps) are set at and check what your stepper motors rev per units are set at.
Seems to me that you have the steppers set at half what they should be at (I think it's that way round anyway) making them travel twice the actual distance required.
For example: (in mm)
A 5mm pitch screw.
Stepper driver at 2000.
So 2000 / 5 (driver / by scerw pitch) = 400.
Stepper rev per unit should be 400.
Then do the fine tuning.
If stepper was at 200 using the above example it would go twice the distance on the machine.