I also have this. I have an Imac with a single user account on it and I've only used the App Store on this machine.
Things I've tried that haven't worked:
* Logging in and out.
* Restarting.
* Removing cache and preferences for storeagent and appstore in ~/library
* Erasing all cookies and cache from Safari (as the App Store is a Webview I thought it was worth a shot)
* Being sure I had no "haxies" that do code injection on my system. I read somewhere that there were problems with the app store and two of Unsanity's offerings, but those were related to downloading programs at all.
* I've sent a message to Apple detailing the problem (and you should too!
http://www.apple.com/support/mac/app-store/contact.html?form=account Under "Specific Request" choose I have another App Store question and fill in the details).
I
am able to delete the applications that show updates under the Purchases tab and download the new versions: Quit App Store, drag applications from Applications to the Trash, restart App Store, go to Purchases, and click install. Cludgey and it negates any benefits to the central location for updating, but it does allow you to update applications. Curiously this seems to point to something on individual machines as the issue as I can download already purchased applications to the same account, but then the problem reoccurs.
Has anyone tried anything else so we can continue narrowing it down? Right now I'm downloading the 10.6.6 Combo Update to try reinstalling (last time I used Software Update) and see if that sorts it out.