I am currently in the process of deploying Microsoft System Center Operations Manager (SCOM) 2007 R2 in our environment to monitor all of our servers. During the deployment process, I noticed that several of our servers that run IIS 6.0 on Windows Server 2003 to host an internal web-based application were not being discovered in SCOM as IIS servers. I contacted Microsoft Premier Support about this and was able to get some assistance.
The first thing they had me try was to reinstall the agent, doing a reboot in between the uninstall and reinstall. Doing this didn't fix the problem. The second thing they had me do was to check the IIS Admin service startup type, and make sure it was set to "Automatic". It turns out that all of the servers in question had their IIS Admin service startup type set to "Manual". I changed the IIS Admin service's startup type to "Automatic" on all of the servers in question, then restarted the System Center Management (Health Service) service. I waited a few minutes, then refreshed the IIS Computer Role view in the SCOM console, and viola! The missing servers showed up, problem solved.
So if you have any IIS servers not being discovered properly in SCOM, you should make sure the IIS Admin service startup type is set to "Automatic", restart the Health Service, wait 5 minutes and check again.
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