Similar problem here
I registered my activation key in the My Account section of the website a few months ago (checked just now, and it tells me I have already registered this key). Even so, when Parallels did its automatic check for an update, and told me one was available, I couldn't update via the app's update dialog - it complained that my copy was not registered (might have been not activated - didn't note the exact wording).
Note that in both the About Parallels window and on the website I am told that the product is registered to me.
I got around the problem by manually downloading the latest build and installing. Still, I thought you should know that the activation/registration (and auto update) process is broken for at least one other user...