GoDaddy whois is not in real time. When you say you complete the checkout process, what do you mean exactly. You complete and pay for the domain, and then GoDaddy sends you an email that it's already registered? Or you are told at the end of the checkout process that it is registered and you don't pay.
Just remember also. If it is a desirable domain, you will never be able to hand-reg it at GoDaddy. It will be registered 1-10 milliseconds after it drops, by a dropcatcher, like Huge Domains, or one of their affiliated companies.