Mac App Store won't allow re-downloading of deleted apps

I am experiencing very glitchy behaviour with the Mac App Store.  The store can't tell when individual apps are deleted, and therefore won't allow re-download.  This has been going on for a while - when I click on the Purchases tab all Apps are still listed as Installed and the button is greyed out - I can't click to re-download.  At the same time, an app that I previously did download and later removed called Cobook won't delete from the computer - after a few minutes to an hour it will re-appear in my Applications folder.
I have done a clean re-install of Mountain Lion trying to fix this problem, however the same problem exists even after a re-install - Apps that had been deleted prior to the clean install are still greyed out in the Purchases tab, and can't be re-downloaded.  The only way that Apps can be re-installed is to use Time Machine backup.  I am concerned that this means that updates also aren't working, since the App Store doesn't seem to know what Apps are on my computer and which ones aren't.
Yes I am using the correct Apple ID assocaited with the purchases.  My purchase history shows up just fine in the Purchases tab, its just that they are stuck showing that they are currently installed, even the ones that aren't.
Mountain Lion 10.8.2, 21.5" iMac (mid-2011).

The problem is possibly worse than I expected.  Since the clean re-install, now any App purchased and downloaded via App Store won't appear in the Purchases tab.  So in other words, although the download seems to work correctly, and the app works, the App Store seems to lose all track of it.  Which is a problem for paid apps.

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