Mac App Store updates keep repeating; won't clear

My Mac App Store updates keep repeating. They won't clear. The update is clearly installed. I know this because the new features in the changelogs are visible in my apps when I open them. The update process itself also works smoothly; meaning the progress bar gradually fills for each item in the update list and displays no errors. The badges will clear, but whenever I go and click on Updates again the badges and all previous updates return. It's very annoying. How do I fix this?

LMAO, I finally figured out the problem! I had completely reinstalled Snow Leopard from scratch and used SuperDuper to make a backup clone of my hard drive beforehand (which I had always been doing for backup). Then before putting anything else on, I had visited the Mac App Store to reinstall some software when I noticed it said I had all my apps already installed. It didn't take long to figure out that the Mac App Store reads any cloned hard drives you have attached and interprets them as installed apps as well. This would certainly explain why it thought I still had the older versions still installed. Huge bug.

Try uninstalling and reinstalling the app from the AppStore.