Comment 5 for bug 269478

dmandell is totally right. I had never noticed this before, but in fact, the shut down menu actually is on top and is clickable, even though it is invisible. This only makes the problem more severe, though.

On the other hand, a few clarifications:

1. This is not specific to Firefox. The same happens if the window in front is OpenOffice, Epiphany,gnome-terminal, etc.
2. The window does not need to be maximized. If the top window isn't maximized, then only the part covered by it is invisible.
3. Whether the Shut Down menu becomes insivible seems to depend a little on what manipulations had been done with the windows before. For me, a way to make this happen consistently is to toggle through the windows with Alt-Tab before clicking on the shutdown button in the panel.