There have been similar reports in connection with Gnome 3, but the problem appears to be deeper. Because of this, I have completely reinstalled my system, several times, installing different distributions with different desktops. I am always experiencing the same ... clicking keeps working on panels, launchers etc. but, at some random point, it just doesn't work anymore on windows and you have to manage them via the keyboard. Logging out and back in solves the problem temporarily, just as you described.
I am really annoyed by this and I'm astonished how this is not a bigger issue ... are there so few people experiencing this problem?
As far as a solution is concerned: I can't offer one, I'm just trying to amplify your cry for help!