I’d go back to basics.
A couple 100mm lines, separate and not connected to each other, 1 X and 1 Y. Or as long as you can accurately measure to eliminate any steps adjustment. The longer the line the easier it is to see an issue.
Rotate your design 90 degrees, see if the oblong shape follows an axis.
And then how did you square?
I don’t know how realistic this is but could it be lost steps? Is the shortened axis the X axis? You could try moving the router at the same speed and seeing how easy it is to make it skip steps by hand. I had this on one of my Y axis in my LR3, it ended up being a loose pulley. In your case pulleys seem fine but there might be some other cause
Thanks for the responses and ideas. I will be looking into these.
As of today, my LR3 project is on hold for a week or two as I need to work on setting up my Christmas digital display and unpacking everything for inside the house.