Does the leadin originate from the inside of the hole, if so change your lead in so that pierces more to the center of the hole, may have to double click on the tool path and drag the lead-in. Check the gantry for backlash and feel for any slop, with the motor on the top of the gantry as well as both sides of the gantry. If slop is greater than .008 it will need to be adjusted to no more than .004 thousands.