Allright, as per your PM your $100 is 40.0 steps per mm, so there is something mechanical going on, since it travels 4.6875" when commanded to move 4.5".
Is your X axis belt super tight ? Does it show any sign of deformation anywhere ?
For the sake of testing whether this is actually something related to the X calibration, you could try adjusting $100 and retrying.
Looks like about 82.32 Euro
Made me lol, thank you 
Belt is new, and tight to where I can barley start the screw threads Wheels are also new just replaced 3 days ago. Eccentric nuts set as well
We now have a perfect square, all the cuts came out to 7/8ths YOU ARE THE MAN What could be causing such a deviation from the factory setting?
I…have no idea, it is quite unusual to have to correct by more than a few tenths of a percent, if at all.
The “40 steps/mm” default value comes from the fact that the Shapeoko uses a 20teeth pulley and a 2mm-pitch belt.
If you would like to get to the bottom of this, can you double-check the number of teeth on the X motor pulley, and then try to measure the actual belt pitch (do you have some leftover you could measure? by e.g. measuring the distance between one tooth on the belt and ten teeth from there ?)
I will pull it apart tomorrow and measure it all and let you know. Thank you again for all your help with this
Belt and Pulley are correct. I just replaced the belt since I had a spare and noticed a small amount of stretch, but this issue had been happening before the stretch. About to run another test and see if the new settings you advised have changed with the new belt
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