Movement Distance Not Correct.

Hello,
recently i tried centering a shaft on my machine using a digitizing probe and i cant figure out why the DRO in emc is reading wrong ?
It reads about 0.040 more then the actual part size , why is this ? I tried setting the tool diameter to zero but it does not seem to help. The manual says its a scaling issue? I'm not sure what that means.

Thanks in advance

-Hans

I'm sorry I could have been more verbose. I was checking X with the probe I had no code so i was just jogging around. I had a shaft in the vise and started on one side touched down, zeroed, and moved to the other side. The diameter was out +0.040". I then checked a parallel in the vise for width along X , This time i got 0.066" over. I checked Z and Y, Z was bang on the money and Y was also out 0.066". I checked for backlash using a dial indicator on X and that resulted with 0.002", which is not horrible. I also made sure no tools were loaded. My hardware includes a Gecko G540 driver, 280 oz 200 step motors (micro step set to 10 as per instructions), and a Taig milling machine. From time to time i have received a real time delay error , but not often, not sure if it matters . The docs said it could be that scaling is set wrong , not sure what that is?