One frequent complaint about the IIS management pack for SCOM is that it raises alerts on servers where IIS is not installed. The two alerts usually seen are “Web Management service is stopped” and “IIS 7 server role is unavailable.”
The IIS 7 Management Pack performs an initial discovery against all Windows 2008 (and 2008 R2) Server computers. It simply checks to see if the registry key HKLM\SOFTWARE\MICROSOFT\InetStp exists. If that key exists, it believes it has found the IIS 7 Server Role class, to which it applies a pair of basic service monitors that check to see if the WMSvc and IISADMIN services are running. These monitors work correctly if those services exist, but can behave unpredictably if they don’t exist.
If you add the Application Server Role to your server, it will install the Windows Process Activation Service (also known as WAS) which came from IIS, but can exist separately from IIS. Since the service came from IIS, installing it creates the HKLM\SOFTWARE\Microsoft\InetStp\Components\WASConfigurationAPI REG_DWORD. That is enough to get the IIS 7 Management Pack to believe it has discovered an IIS 7 Server Role, and apply the two service monitors mentioned above.
2 possible fixes are:-
1.Disable the IIS7 discovery rule and create a new one
2.Extend the IIS 7 Computer Role class, and then create groups that contain instances of it where WMSvc and IISADMIN actually exist. Then use those to override the monitors. This method is more complex, but makes less invasive changes to the management pack in case a future release of the IIS 7 management pack
FULL EXPLANATION AND FIXES CAN BE FOUND VIA THIS LINK.