Shaun, if Windows worked correctly then closing Cardbox before upgrading it would indeed be enough to ensure an upgrade without reboots. (If you are upgrading a copy of Cardbox held on a file server, you have to close Cardbox on every workstation that was using it).
With "real, existing Windows" there is a problem, as Bert has pointed out. I've added a page to the Cardbox knowledge base that discusses possible reasons for the reboot and suggests ways in which it might be avoided:
http://www.cardbox.com/support/kb/installReboot.htm