You might have to adjust your steps . I had a similar problem with a home built cnc . My x and y had differet pitch screws so screw resolution was critical . I used a 3 .0 inch gauge block and zeored off one end then indicated the other edge . Then adjusted the steps to make the move were it had to be .Then my cicrles were round . I did have to check ball screw preload , end block supports , shaft couppling , thrust bearings , ballnut carrier , everything connected to saddle screw and machine base abd table .If you tell the machine to move 3 inches in y dose it move three inches ?