If I have a Download window in the background and I have a webpage as the frontmost window, when I go to the menu and ask for the Download window, WebKit will return another empty Download windows.
The Downloads window is part of the Safari application, not of the WebKit framework. Bugs in Safari should be reported to Apple at http://bugreport.apple.com/. Closing this bug as INVALID to indicate that the problem is outside of WebKit.