I would take a look at the coolant. It could be that you are welding a bit to the tap and that's what is causing the oversize. The other possibility is occasionally a chip gets stuck in the tap and makes an oversize hole. Maybe an air blast to blow off tap and the part to make sure they are clear? Is it possible to use a forming tap rather than a cutting tap?
Is it possible to use a heli-coil to save the part?
EDIT: I had another thought. Are the hole sizes on the offending holes correct? One of the old tricks to oversize a drilled hole was to drill through a rag, you can do the same thing with a tap. Some of the rag fibers would be pulled into the holes with the drill bit and would cause a slight oversize, a chip stuck in the drill bit might cause the same problem.