I have to start out by saying that I am not sure if this is a Gnome 3 problem or a Gnome 2 problem as well, but it has forced its attentions on me by virtue of the way in which Gnome 3 encourages you to work, that is, in the 'mobile phone' mode where applications are left running rather than shut down. Now in the past I shut down everything, all the time, and frequently cursed myself for doing so when I found that I wanted the same program open again 5 minutes later, so I have found that this way of working has been a time saver on occasions, but it also leads to this shutdown problem. I will nearly always have a terminal open, frequently logged in as root, and maybe a root file manager as well, and if I don't shut these down prior to closing down the machine it leads to this problem where Gnome says that I can't shut down without giving my password again because somebody else is logged in. Nobody else is logged in, I just have a root terminal open that is all.
Before I give you the solution to this I should perhaps point out that if you are on a system where other users really are logged in then it is not a good idea to implement it.
If it bothers you this is how you get rid of it.
You need a root text editor or file manager or terminal, and navigate to /usr/share/polkit-1/actions and open org.freedesktop.consolekit.policy and look for the entries:
You need to amend them so they look like this:
<description>Stop the system when multiple users are logged in</description>
<message>System policy prevents stopping the system when other users are logged in</message>
<description>Restart the system when multiple users are logged in</description>
<message>System policy prevents restarting the system when other users are logged in</message>
The line to add is in red.
You will now be able to shut down or reboot without providing a password.