"The problem would therefore appear to a gnome problem, does it's logon manager also use /sbin/reboot?"
Yes. I am in KDE now so I can't look through the gnome control tables to find out where gnome specifies what command to use.
Another way to reboot from gnome is to issue /sbin/reboot from a shell command line. You may have to su first.
Be prepared. Create a LifeBoat CD.