If you are doing this on Win2k8 (not sure about other OS's) - and you turn on IIS 6 Metabase Compatability... like so:ServerManagerCmd -i Web-Metabase and you turn on:IISPREFERLEGACYOBJECTS=1Then you will NOT get the hokey ghost VMs. (whew)
I am experiencing the same problem. IS9 creates the web application directory just fine, but it adds a virtual directory beneath it which is a shortcut to the same physical path. How can I keep these from appearing?