All I did was change a registry setting (or maybe it was a gpedit) to prevent automatic reboots. That was enough for me though, as I didn't appreciate my running apps being shutdown during the night.
Can you maybe recall exactly what u did to stop your computer to automatically shutdown(and up)?
I "resolved" the issue by dual booting. The second os(prev ubuntu, going to deb) changes something that takes away win ability to automagicly turn on my machine for updates.