Comment 21 for bug 838792

I had the same bug, and in my case, I manually stopped the plexmediaserver (which I had manually installed) before trying to shutdown. This solved the problem. My guess is that there is a daemon process running as a user that gnome-session sees as being logged in. I'm not sure how gnome-session determines which user sessions are safe to terminate, but stopping this process let my machine shutdown and reboot normally.

I'm not really sure this is a bug with gnome-session so much as it is a bug with other packages starting daemons that show up as actual users.