move error in MACH3

We have a Grizzly mini mill with 276 ozin steppers, Gecko 540 (24v) supply, and MACH3. We are making egg shaped circles and want them to be round.

We have calibrated the axis's and they are both right on (and very similar steps per inch numbers of 15984.xxx and 16000.xxxx. And we have redone the backlash, (home made plastic nuts on ACME threads) X was 0.001 and Y was 0.009. And we have restarted MACH several times to and confirmed that the settings have changed.

HOWEVER, when we go to MDI in MACH and tell the X axis to move 0.5", it actually moves 0.455" - and is pretty repeatable (+/- a thou or sometimes 2).

Interestingly (and frustratingly) when we do an 8 hole bolt pattern, and measure the major and minor axis's and subtract the smaller from the larger, we get a difference of 0.046"... note that 0.5-0.455 = 0.046. We must have some setting messed up, but just can't find it.

Any help would be great!
Thanks,
Chuck