I have been experiencing this as well with Intrepid on a D600 as well. In fact I didn't realize the problem was related to the use of Fn + hotkeys to change the brightness, until googling the issue. When the issue occurs, the menus in the panel will not open. Clicking the mouse will highlight the Application Places menu, etc, but it won't open until I switch a console and then back to X with ctrl-alt-f1, and ctrl-alt-f7. Clicking on some of the other icons in the panel will work, but results vary.
I have been experiencing this as well with Intrepid on a D600 as well. In fact I didn't realize the problem was related to the use of Fn + hotkeys to change the brightness, until googling the issue. When the issue occurs, the menus in the panel will not open. Clicking the mouse will highlight the Application Places menu, etc, but it won't open until I switch a console and then back to X with ctrl-alt-f1, and ctrl-alt-f7. Clicking on some of the other icons in the panel will work, but results vary.