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MAS always updates my purchased apps. I have however heard of it declining to do so if you have, on some attached hard drive, a newer or same-version binary or installer. But have had no problems with MAS myself. YMMV.

Why the downvotes? And no, clicking "update" did /not/ work!

Found the solution: This happens if you have "Macintosh HD" listed under the privacy tab of Spotlight's System Preferences.

http://bugreport.apple.com/

Thank you. Good idea; reported.

There is an obscure button in the App Store called Updates that will update purchased apps.