I switched from gnome-shell to elementary-desktop while waiting for a solution, and the problem disappeared.
So it is really a gnome-shell (or extension or whatever) problem. To mention: I have the EXACT same beheaviour as the OP, meaning the mouse clicks are not working INSIDE the open windows. But i can still click on items in the Activities screen and the top-bar and still type into already-active textboxes in windows. I think comments from some people here seem more like a general mouse- click not working problem. Not really sure if these are two different issues or not ... As i can see it seems a confirmed gnome-shell bug and upstream is working on it: https://bugzilla.gnome.org/show_bug.cgi?id=762193 -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/1181666 Title: gnome-shell randomly blocks mouse clicks from working in app windows To manage notifications about this bug go to: https://bugs.launchpad.net/gnome-shell/+bug/1181666/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs