This sounds an awful lot like
https://bugs.launchpad.net/ubuntu/+source/policykit-1-gnome/+bug/540247
It may be a duplicate.  The only problem is in the end, my situation
doesn't appear to be exactly the same.  For me,
/usr/lib/policykit-1-gnome/polkit-gnome-authentication-agent-1 is not
running.  If I start it manually in terminal, everything goes back to
working as expected.

jonat...@jonathan-desktop:~$ /usr/lib/policykit-1-gnome/polkit-gnome-
authentication-agent-1

(polkit-gnome-authentication-agent-1:11849): GLib-GObject-WARNING **:
cannot register existing type `_PolkitError'

(polkit-gnome-authentication-agent-1:11849): GLib-CRITICAL **:
g_once_init_leave: assertion `initialization_value != 0' failed

Ok so there everything is working as expected.  If I quit the terminal,
things go back to the way they were.  I then tried some of the debugging
near the end of the linked bug report:

jonat...@jonathan-desktop:~$ cat 
/etc/xdg/autostart/polkit-gnome-authentication-agent-1.desktop
[Desktop Entry]
Name=PolicyKit Authentication Agent
Comment=PolicyKit Authentication Agent
Exec=/usr/lib/policykit-1-gnome/polkit-gnome-authentication-agent-1
Terminal=false
Type=Application
Categories=
NoDisplay=true
OnlyShowIn=GNOME;XFCE;
X-Ubuntu-Gettext-Domain=polkit-gnome-1

jonat...@jonathan-desktop:~$ ls -l 
~/.config/autostart/polkit-gnome-authentication-agent-1.desktop
ls: cannot access 
/home/jonathan/.config/autostart/polkit-gnome-authentication-agent-1.desktop: 
No such file or directory

jonat...@jonathan-desktop:~$ cat 
~/.config/autostart/polkit-gnome-authentication-agent-1.desktop
cat: 
/home/jonathan/.config/autostart/polkit-gnome-authentication-agent-1.desktop: 
No such file or directory


As you can see, I don't have the 
.config/autostart/polkit-gnome-authentication-agent-1.desktop file in my home 
folder.  (Renaming/deleting this file solved that user's problem).

-- 
Policy Kit Unlock not functioning
https://bugs.launchpad.net/bugs/568748
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