I have been having issues with my keychains where the "XXX app has been updated. Do you want to allow the new version to access the same keychains?" dialog would keep coming up -- even after clicking Change All. No matter what I would do, the window would come back and end up hanging forever, forcing me to reboot.
After hours of frustration I found this article on unsanity.org that contained the fix. Open Terminal and type:
sudo mv /var/db/CodeEquivalenceDatabase \
/var/db/CodeEquivalenceDatabase.old
That resets the database used to determine what apps can access the keychains. The problem is now gone!
Mac OS X Hints
http://hints.macworld.com/article.php?story=20070608010326883