I have had the same baffling issue lately, and I still don't have a positive identification of the cause for the puncture: I just got the second puncture on the inside (toward the spokes) of the tube. I have adhesive-backed cloth rim tape, so I'm sure that's not moving; I installed the tube by hand, and I'm certain it wasn't kinked or nicked by a screw-driver, etc. There was absolutely nothing in the tread or in the inside of the tire.
Two factors were common on both days I experience this kind of flat. I had just topped up the air pressure to 90 psi, and the day was hot (I live in Texas). Today, I rode 17 miles to work on the tire in the morning with no problem. Less than a quarter mile into the ride home in the afternoon, the tire went flat. It was similar the last time, too. I have to assume that getting out on very hot pavement (the asphalt was soft and melting in places) caused the tire pressure to increase. I'm not sure of the physics, but it's possible that that this would cause the tube to develop a hole in that location.
I think the solution in my case is to keep the tires inflated to a lower pressure (as measured cold by the tire gauge) when it's this hot out because the pavement is going to heat them up and increase the pressure.