Odd Hole Pattern Issue

I have created a hole pattern using the Point method in the dropdown menu (Pattern --> Point --> Sketch).  For some reason when I try to have the hole have a counterbore, the hole locations shift offcenter from the original sketch location.  Without counterbore it seems to be fine.  The pictures attached are me simply changing the hole type to/from counterbore.  I did not modify the sketch nor is there anything that would link back to it (that I have put in). 

I've had this happen before on other parts but it seems to be random.  I'm modeling this part in aircraft coordinates so the face is at an angle with respect to the original coordinate axes/planes.  Could this have something to do with the issue, even though relative to the surfaces all the features are perpendicular?