I am one of those people that does not believe in using Mach3 calibration - if you can't calculate the settings and get it right, then you might be covering up a more serious problem. But I'm probably in a minority here...

Back to the original problem - can you describe a bit more exactly what you are doing? Given that you are quoting dimensions to .0001mm, I'm guessing that you are taking these figures from the Mach3 DRO?