CMDB - Discovery not detecting IIS and Websites

CMDB - Discovery not detecting IIS and Websites

What would cause network or agent scanning discovery of a WIndows IIS Server to detect all software except IIS and the hosted websites?  We heavily use IIS website hosting for our crititcal business component websites and their discovery/scanning for changes is critical to populating our CMDB and automating our CMDB auditing.

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