Hey woodsnipper,
Of course the diagonals alone do not make the rectangle. The sides must be equal to, i.e. the X front and the X rear must be equal. This normally is ensured by shifting the thy X Rail back and forth while the controller ist off and one front foot and one rear foot are loose. If you say you made minor adjustments afterwards, you got to re-check this X=X’ then.
And on the other direction, the left Y length and right Y length must be equal too – there I assume it is, because I think Onefinity saws the rails to a defined length and mounts the feet to the same distance. I hope they do.
My next question Tom already asked, can you run a program to mill a square?
How much do the front side and the rear side of your trapezoid measure exactly?