You're exactly right, Hood. In my experience, usually the drill chuck and drill bit run out a little. Also, if the bit is a little dull, it will cut over-sized holes. And after you tap the hole, it opens it up a few thou. So, with all that, I'm not surprised the holes are .007 over. Most tap charts are for 75% thread depth which indicates Class 3 fit tolerance. To be able to hand tighten most fasteners, this is the most widely used fit tolerance.

AA