Perhaps your web server is providing the correct SCRIPT_NAME,
and the problem is introduced in Publisher.process(), which attempts
to work around a common, similar SCRIPT_NAME/PATH_INFO problem in
a way that would make matters worse for your setup.

Here's the code I am talking about:

     def process(self, stdin, env):
         """
         Return a Hit with a complete response.
         Subclasses that want to customize the Hit class may do so by
overriding
         this method.
         """
         if env.get('SCRIPT_NAME') and env.get('PATH_INFO') == '':
             # The "script" here is your QP application, so the
SCRIPT_NAME
             # should be the part of the url, after the host name, that
             # causes requests to be handled by your QP application.
             # The PATH_INFO part of the path after the SCRIPT_NAME.
             # We expect applications running at the top of the URL
space
             # to get requests where the SCRIPT_NAME is the empty string
             # and the PATH_INFO starts with a '/'.

             # Your HTTP server is not providing the expected CGI
environment.
             # The full path part of the URL is being put in the
SCRIPT_NAME.
             # We'll try to make it work anyway, but we are assuming
here
             # that your application is running at the top of your
URL space.
             # If you want your application to run somewhere else in
your URL
             # space, you must change your server so that it provides
the
             # correct environment variables.  Alternatively, your
publisher
             # class can override this method and hack the
environment as
             # needed to fit QP's expectations.
             env['PATH_INFO'] = env['SCRIPT_NAME']
             env['SCRIPT_NAME'] = ""
         hit = Hit(stdin, env)
         self.process_hit(hit)
         return hit

In your case, I think you could try overriding this method and
changing any empty PATH_INFO to "/" and removing the "if" statement that
appears above.

Even easier, perhaps, would be to put a redirect in your web server
config
so that '/app.cgi' always redirects to '/app.cgi/' before qp sees it.