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Trying to measure a 3mm hole with a 1mm probe

I am trying to measure the position of a 3mm diameter hole using a 1mm probe tip. I tried using the auto circle measure tool and it positioned the probe incorrectly. It didn't move over the hole, but was off by about 2mm. Why would this happen? The hole is dead on position and the part matches the model to within .001". I measured the alignment with a different probe on three square faces of the part. Would this impact where the machine thought the hole is? Is there something wrong with the hardware? Both probes were calibrated before measurement with no errors. Any help would be appreciated. 

Also, I still need to measure the hole, but taking hits moves the probe too far back. how do I change it so that the probe can measure the 3mm hole?