Hey Mark,
have you ensured that your machine is rectangular (“squared”) (bar gauge) and coplanar (“not twisted”) (fishing line method) .
In both cases if it is not accurately adjusted, not only you can get parallelograms instead of rectangles, but also workpieces with a twisted surface. Surfacing the wasteboard will not help against lack of coplanarity (twisted machine base), the machine will only reproduce the twist on the workpiece surface. Also if any of both is not accurately adjusted, the Y movement can block.