Comment 3 for bug 494096

I've seen this as well. I also have Compiz effects turned off. For me to replicate this easily, I need only maximize my Firefox window, Maximize a terminal window that was previously not maximized (I do so by double-clicking the titlebar), Alt-Tab back to Firefox, and if I double-click the titlebar or click the minimize button or click the normalize button or the close button, the click affects the previously active window, in this case the gnome-terminal. So if I minimize the Firefox window, it instead minimizes the gnome-terminal window. I moved the file .gconf/apps/metacity out of the way, rebooted, and it hasn't affected anything. If it matters, the metacity folder did not get recreated after reboot as I would have expected.