There are several variables to your questions.
What Software are you using?
What motor drive are you using?
What is the runout of your spindle/router?
Are the parts uniform? i.e. is the 49.4 x 49.7 square and uniform, or does it vary and the part ends up trapezoidal shaped?
Is the error repeatable or does error vary?
True, it would seem that a non-concentric pulley would seem to introduce a variance in position, but the variance should be repeatable over the range of movement.
Many possibilities exist.
-=Doug