@phildoyle
Please check the following on the software side:
The correct steps/mm are set for your ballscrews pitch in config.g
If you had backlash compensation enabled for your old leadscrews, disable it for now. Ballscrews should have relatively low backlash.
You have set the correct tool diameter in your program
Confirm the diameter of the physical tool
Since the holes are spaced correctly, it is unlikely that you are loosing steps. But you can check the following to make sure it is not a mechanical issue:
See if the ballscrews are securely coupled to the motors
See if the ballscrew bearings have any play or are loose
Reduce your cutting feed and reduce your depth of cut to see if high feed speeds are bending your machine
Check if your motors are loosing steps: Position the spindle at a point outside your working area. Get something to mark this position. A dial indicator would be optimal. Mount the dial indicator so that it is stationary on your machine. Set the spindle against the dial indicator in die direction of the X or Y-Axis. Zero the dial indicator and note down the machine position. Then run your Program. When the Program is finished, move the spindle to the previously noted position. If the dial indicator is still close to zero, there should be no lost steps.