I had this happen on a flight from SJO to ATL. I went to pick my seat while booking and there were only 3 or 4 seats left, all middle (767). I thought about it and decided to see if I could get a mileage or SWU upgrade. When I spoke with the agent he stated that I should save my miles and certs because it looked almost certain that I would clear automatic upgrade. I said "OK, I just didn't want to get stuck in the middle seat." He responded that he could put me in a window seat no problem, just in case I didn't get the upgrade, and assigned me a window on the spot.

Not sure what happened, but might be worth a phone call for you.

SR