I've seen this kind of thing happen once or twice, but never consistently. Can you get this to happen each time you do a reset_window_layout (tbResetAll is an alias for this command)? I'm wondering if something else has focus (e.g. notification window I saw in your attached screen shot) during the reset_window_layout perhaps?
From your screen shot, I can see you have other problems (Class tool-window is not visible).
++rodney