I've got my XenDesktop setup on a 2k8 server running on the Default Site under IIS. I just installed WSUS 3.0 and and was able to put the admin access on it's own website, but the self_update still runs on port 80. Which causes my citrix web access to break and wsus admin to break as well.
I think that WSUS selfupdate has to run on port 80? I'm not sure if it can be moved. I've been looking for an answer for 4 hours.