As additional feedback: I have been using my system normally, and had noticed that the shadow dissappears from time to time, but I didn't exactly know when or where or what had caused it to dissappear.
Just now, the shadow was not present, and dropping down guake made it appear. My unconcious knee-jerk reaction was to hit F12 to fold the shadow guake menu, but I hit the wrong button. When I hit the button, the window focus was on Chrome, and the button I hit was F11 (full screen mode in chrome). When I got out of full screen mode, the guake shadow layer was gone.
