App Store Updates staying in queue after installation?
Normally restarting should fix that.

This could a problem of broken permissions that can be repaired in disk Utility.

If above did not work:

It also sounds like your problems are being caused by corrupted preference files. Located in ~/Library/Preferences/

com.apple.storeagent.plist
com.apple.appstore.plist


Quit all applications on your Mac, delete the two files above, and reboot your Mac.