Just thought of one other thing like this that someone reported a while back using Win 2003/IIS 6, they had a misconfiguration in the handler mapping .aspx extension for ASP.NET where the "Verify that file Exists" was checked so if the file does not exist on disk IIS returns a 404 without handing the request to ASP.NET.
These screen shots are what they guy sent me showing the box he had to uncheck
The reason is pages you create don't really exist on disk, they are all served by /Default.aspx?pageid=x but through the magic of url re-writing we have friendly urls. Those friendly urls do not correspond to files on disk so IIS needs to just let ASP.NET handle the reuest and ASP.NET can return a 404 if it can't handle the request.
Hope it helps,
Joe