I ran into a problem where the Mac App Store said that a particular app (Numbers in this case) was up to date, but whenever I launched it I would get an older version. I finally did a search across the entire computer and found Numbers.app in a folder on an external drive. I have no idea how or why it was installed there instead of on the local hard drive. So I moved it from there to the Applications folder on the main internal drive and re-created the dock shortcut and now the correct version launches.
The problem is, now when I go to the App Store it says there is a new update available. So it appears that the App Store wants to use the external drive location and now that I deleted it from there it wants to put it back. Obviously I don't want this to happen: first of all, if the external drive goes away I would lose the app, and second, every time there is an upgrade it is going to cause more problems.
So, how do I get the App Store to correctly recognize that Numbers is installed in /Applications, not on the external drive?
Best Answer
Figures I found someone else that runs into the same problem as myself and no one has answered with a solution yet.
What I can offer is a work around for now until someone chimes in with a better fix, because I have an external drive that I use as backup by cloning my OS X partition. So when I decide to format and reinstall fresh I run into the same problem as you except I can't even install the apps because it says they're already installed.
Simple and Quick - Just disconnect the drive and restart the App Store, it will refresh with the correct information.
-Idea's I've been kicking around, but have not given it much more thought or a go.
I was going to make the drive hidden by putting a "." as the first character of the partition name, but I kept running into another problem (can't remember).
Anyways I hope this will work for you since anytime I've ever ran into the issue i've always resolved it by disconnecting the drive.
Good Luck! -Mac