Oh man, I have been using Configuration Manager with System Center Advisor and it never reports any problems, but I have never been able to get the software catalog to connect to the Application Server.  I troubleshot this for about 2 weeks, then i gave up.  No matter what I do I cannot get the Application Catalog Web Portal to work correctly.  I have made sure that I have all the prerequisites and I have also reinstalled the web site and website svc roles multiple times.  I think it is a problem with the connection to SQL server.  Anyway, The Advisor was easy to set up but I wanted it to help me fix this problem, and it did not give any alerts yet.