When I use the "Reopen all windows from last session" command in Safari/Webkit.app [Version 3.1.1 (5525.18)] it creates an invisible window named "Untitled" with nothing in it, according to the Activity window. I've attached a screen shot where this issue can be seen. You can see the Window menu only shows the page with the Wikipedia open - no other windows exist. But the also-visible Activity window shows another "Unitled" window exists also.
Created attachment 21316 [details] Activity window shows the Untitled 'ghost window', but Windows menu doesn't.