I experienced the same issue after going back to stock and coming from a custom rom. The following day however i tried to check for updates again, and this time it came back with "you are already runing the latest OS" message.
So basically i think it's just a matter of waiting a period of time for your phone to properly register it's version or whatever with the carrier.
Give it a day or two and try again, it should work.
Haha funny that. It took 3 days but I just hit it again and got that message. Last night it was still "not registered". I know, I already had upgraded manually, just wanted to make sure I'd get the prompt when official JB came out. Thanks!