People do not know but the IISReset command can cause some settings to be lost.
The IISReset command line tool waits for a normal shutdown of the services before it starts them again. Because of the number of services that are dependent on the IISAdmin service, the shutdown may not occur in a timely manner. When this happens, IISReset forces the shutdown of the services. This can result in metabase changes that are not saved properly.
Today at a customer site when I ran the Remote Conectivity Analyzer (ExRCA) Exchange 2007 server it was complaining about Annonymous authentication being enabled.
The Initial Anonymous HTTPS request didn't fail, but Anonymous isn't a supported authentication method for this scenario.
To fix this we simply need to disable annonymous authentication on the RPC web application in IIS.
When disabling annonymouse authentication and running the IISRESET command it simply re-enables annonymous authentication.
To commit changes while still restarting IIS6 run the following commands:
net stop iisadmin /y
net start iisadmin /y
If you notice now, the changes has been permanently committed to the IIS6 metabase.
For more information about this problem please see the following knowledge base article: