This happens to me every time I have a CO flight (either upgraded or not, but usually when its upgraded) on a UA reservation. I can't check in and no one can tell me why. Well, the good news is that you're upgrades are still confirmed. You just have to see a gate agent at the airport to obtain your boarding pass. Its usually pretty hassle-free. Since you're upgraded, definitly visit the first class or business class gate agents since you don't want to have to wait in line.

Note: you can't check in using the kiosks at the airport either, that won't work, you'll get an error message. It has to be a human.

I think this is a temporary problem.