Customer was noticing that the ServiceDesk Service Account using w3wp.exe was associated with the deletion of the C:\Windows\System32\inetsrv\config\ contents. This is caused ServiceDesk to stop functioning.
The customer had orginally installed Servicedesk, with all of the default applications. Later, a new version of SD.EmailMonitor (SD.EmailMonitorMulti) was installed, but not as web applicaton. This was installed as a Windows Service. The two versions ended up colliding, causing the changes in IIS.
Removing the Virtual Directories in IIS for the Web App version solved the problem
Servicedesk 7.5 MP1