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If your screw isn't all the way in, you won't get an accurate measurement. Make sure you've bolted the screw firmly into place. The head of the screw should be level to or slightly below your project surface. Don't drill too hard -- if you strip the screw, it will be almost impossible to remove. Look on the other side of your project surface. If you can see or feel the tip of the screw poking out, it's too long and you'll need to cut it to fit. You don't need to take the screw out of the surface -- you can cut it right there with a wire stripper.
Make sure the screw is fully sunk into the pilot hole. Check the backside of your project to see if the screw is poking out.