Always make sure to disable the windows update services before starting any significant software upgrade. We found out the hard way that process such as a long running database backup does not handle kindly to spontaneous server restarts.
Its one of those thing that can easily slip through the cracks but have a large impact in your deployment. So always make sure to add this to part of your per-requisite checklist.
Personally I use the net stop "windows update" command as it is only effective until you restart the computer/service.