I had several machines not checking into a new WSUS server. After some digging I discovered that after cloning machines from the same image that a registry key was preventing the machines from joining the WSUS server. You see, they all had the same SusClientID key and would compete for the connection to the server.
I just upgraded our systems with VMware's ESX server. When installing you can use SQL 2005 Express, but the downfall is that there isn't an automated backup in the management studio. So I created a batch file that would call a SQL query.