This has been happening to me. Especially with firefox, thunderbird, skype, and pidgin running. I can have all the windows open, none of the fully maximized and I am unable to get focus on any of them. Occasionally, I do manage to get focus on a window, but the menu at the top of Unity displays the default desktop menu or the menu of the last application to have focus, Not the application menu.
This has been happening to me. Especially with firefox, thunderbird, skype, and pidgin running. I can have all the windows open, none of the fully maximized and I am unable to get focus on any of them. Occasionally, I do manage to get focus on a window, but the menu at the top of Unity displays the default desktop menu or the menu of the last application to have focus, Not the application menu.