Yes!
I would first r/o a problem with stepper calibration. To do that, I would make objects of several sizes. You mentioned making a 3x6 inch test piece. I would make a 6x12 and even an 12x24 test pieces. If you errors remain .0325 inches, that would tell you that your steppers are properly adjusted.
to r/o backlash problems, I would approach a line from opposite directions and make cuts. If the lines are offset, then you have a problem with backlash. If the lines are even then you have ruled that out.
After ruling out above, I would look at software. One common error is to have offsets set incorrectly. Is it possible that you have a .0325 offset set in your profile cuts?