I had exactly the same problem on a new machine.

First: Check the run-out of the tip of the probe. I put a test dial indicator on it to verify run-out. You should actually be able to visually verify - 20 mils is easy to spot. Just rotate the probe in head while having a vertical surface close by.

20 mils is half of 40, which is 1 mm. I had to change the probe ball diameter somewhere in Mach3, but I can't remember where. I think it was set to 4 mm, and the probe is 3 mm (measure and verify).

Geo