Description of problem: After updating my FC12 box on Jan 21, PackageKit no longer gives (for a normal user) the authentication dialog where one should enter the root password. It just bluntly says that authentication was failed and it is not possible to install anything (unless one goes to command line/root & yum). I am not sure if this is a PackageKit problem though, running, for example, System -> Administration -> Firewall also fails to start complaining Error: "org.fedoraproject.slip.dbus.service.PolKit.NotAuthorizedException.org.fedoraproject.config.firewall.auth: " So this is probably a problem with all applications requiring root authentication.
Is polkit-gnome-authentication-agent-1 running in your session ?
It was not and I noticed that it had been somehow disabled from the startup applications. No idea how that happened but since I don't see much "me too" comments here, I suspect this is something specific to me... I re-enabled it and now authentication works correctly.