Just some info for anyone wanting to add Clonecd to their cd.
You can use the "setupclonecd####.exe /S" (in my case, version 4331 from slysoft.com) option for silent install.
Because there's no way via switches to get around the problem of the "reboot now?" box coming up, I found an alternative. Use the sleep.exe command utility to rest it a few seconds while it's installing, then kill the "setupclonecd####.exe" task and it'll kill the box.
And if ya definately don't want the box to be seen, maybe can start another little process just after running the setup to take away focus? Any idea on what might fulfill that?