I have been a mac user since the days of the Mac LC. Still, just on occasion, I get befuttled. Rattled. Confused, and frankly it does not help that I am also stupid. I was able to bring it all back when I turned on spaces. When the application was running, sometimes the window would disappear though the menu was still visible. I would try to open a new window, and nothing. I would try to quit the application, restart it and still only see the menu but no window. Odd, and it only happens on my MBP, but NOT on my MB or iMac.
My LC does not seem to be affected either.