I'm using Sabayon Linux and the Gnome 3 desktop. I'm getting a random bug which prevents me from clicking inside windows. I can mouse over the activities to bring up the window selector and I can click on a window to select it, but once that window is brought up my mouse clicks within it don't register. Obviously this makes my computer very difficult to use.

Clicking on the menu in the top-right of the screen still works so I can log out then log back in, but having to do this several times per session is frustrating. I don't know how to even begin to diagnose this, so any assistance would be very gratefully received!

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!

Thanks for posting Ciginator. It's a shame that nobody can advise on how to even diagnose the problem, let alone solve it. Thus, I have abandoned Gnome 3. I'm using XFCE now, and I'm a lot happier!