CoreXY Calibration Issue
Oscar's answer is the correct solution to this issue. My printer was printing skewed and there is a built in correction for this in Marlin. Unfortunately the X5S does not have a boot loader and I don't have an ISP programmer (yet), so I am unable to re-flash my board at the moment.

In the mean time I created a software fix for this issue. I used a script to add a Affine Shear Transformation to the stl file. This adds a reverse skew to the model so the print comes out (closer to) square. Basically read all the points from the triangle mesh (STL file), apply XY shear transformation preserving Z, re-save the STL.