If you are still having problems, to get the DROs calibrated just go to the config menu and select motor tuning. At the lower left corner enter in the Steps per box the correct number of encoder counts per inch (or mm if in metric). Also set the maximum velocity you want (this becomes the rapid move velocity), and an acceleration value, and be sure to click SAVE AXIS SETTINGS button or the changes will not be saved. On my machine I use 20000 counts per step, 150 for velocity, and 100 for acceleration, your results may vary. You can also set the duration of step and dir pulses between 1-5 usec if you are using this type input for your motor amplifiers.
Then select the Y Axis button and repeat, then Z axis, etc. It is a good idea to make an actual move and measure the distance with a dial indicator or separate DRO if you have one on the mill. You can fine tune the steps per value as needed.