It wasn't 10%, it was actually 20%.
As I said, rectangles and squares were perfect, only circles were a problem. I was doing some CAM tests and happen to order two rectangles, 100mm x 50mm. One was aligned to the X axis the other to the Y axis. Lo and behold, they came out different sizes !!
I checked my thread pitch on both axis and found that my supplier had sold me two different pitches on the two different days I shopped for parts !! X axis is 1.5, the Y axis is only 1.25. I changed my Config>Motor tuning and presto my circles are circles. I didn't pick it up when making the nuts as I used HDPE and the rod just cut it's own thread.
Just goes to show, never assume.