I would need more information to exactly answer you, but if I understand you right, it is possible that all but two holes are positioned OFF of the face of the body you are drilling. If this happens, I believe UG might still create the features, even though they fall off the part, and are actually non-existing (although I was not able to verify that in NX1). Another thing to check is if they are created inside a body, and are actually "swallowed up" by the body.