This seems to be a common problem with Anytime Upgrade from Windows 7 Home Premium x64 to Ultimate x64.
I have done the upgrade for my friend's laptop and I got the same error and the upgrade did not complete for atleast three to four times. Then went to the shop where we purchased the Anytime upgrade kit. The shop assistant has tried it infront of us and it got upgraded to Ultimate.
Later on with this experience, I have tried upgrading my Home Premium x64 to Ultimate x64 on my laptop. I again got same error. Upon restarting the system, however it got connected to Microsoft website, downloaded some updates and later on completed the transition to Ultimate x64.
Since then my system is showing the Windows 7 as Ultimate with the additional Ultimate features available (Bit locker, Additional Languages support etc.)
So you can ignore the initial error before the upgradation. As long as you have the Ultimate features available to you and the system is working fine, nothing to worry...