Others have much more experience with domestic upgrades than I do, but this did happen to me once, and it turned out that I had actually already been assigned a seat in F, it just wasn't showing up on my screen. And for reasons I can't recall, it was not immediately apparent to Customer Service on their screen what had happened either, though they eventually figured it out. Have you tried logging all of the way out of your browser and logging back in? You could also consider calling asking the agent to manually check you out and back in to the flight. I don't know if that will potentially screw up your current upgrade priority though. Good luck!