Thanks! Seems that PolicyKit is running correctly. Does
sudo killall polkitd; sudo /usr/lib/policykit-1/polkitd
report any error?

It may be that you're not detected as an active user, which could come from a 
ConsoleKit problem. Then, connecting via VNC would actually matter, if there's 
a bug in that part. You can edit 
/usr/share/polkit-1/actions/org.freedesktop.SystemToolsBackends.policy, find 
the lines
    <defaults>
      <allow_inactive>no</allow_inactive>
      <allow_active>auth_admin_keep</allow_active>
    </defaults>
and put "auth_admin_keep" instead of "no" on the <allow_inactive> line. You may 
also set both to "yes", but don't forget to revert this change after you tested 
it. This should allow users to change settings without authentication, the 
first line is for users not detected as active (as the name says :-p ). Hope 
this helps...

-- 
User account lost permissions after Karmic upgrade, breaking all audio
https://bugs.launchpad.net/bugs/477832
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