Ive always found the axis calibration to be less effective than a calculator, mostly because it does not calculate to enough decimal places. To calibrate better I simply work out the steps per mathematically. Place a dti at one extent of axis travel, and run the axis from - extent to the dti, if it's off I simply add or subtract step units incrementally from the end decimal places and repeat until it is within the desired accuracy.
It's the only way to get it spot on imo, re entering the travel into the axis calculation will loose you decimal places of accuracy, you want it to around 9-10 decimal places.