Marcus Naeher has the solution in #17 above

For LXDE it is true as well that the PolicyKit  Autostart has been
unchecked by default in the latest version of Ubuntu/Lubuntu If you
check this box and restart, Synaptic package manager will start from the
launchpad menu and will ask for Authentication and all is well. Here is
his answer quoted below:

"I have found the solution by happenstance:

(I am using XFCE in German, so maybe the wording I describe here is not 100% 
accurate)
In the XFCE settings menu -> Session management -> Automatically started 
applications, there is an Item "Policykit Authentication Agent".
This was unchecked. Re-check, reboot (probably logout and login is sufficient), 
and it is back working.

But: I am absolutely sure I did not remove the check. On one of the
affected computers, I have never been in this dialog before."

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You received this bug notification because you are a member of Ubuntu
Touch seeded packages, which is subscribed to policykit-1 in Ubuntu.
https://bugs.launchpad.net/bugs/976638

Title:
  pkexec does not find any authentication agent

Status in PolicyKit:
  Unknown
Status in policykit-1 package in Ubuntu:
  Triaged

Bug description:
  I am using xubuntu, but I am pretty sure that other variants are
  affected too.

  My problem started with being unable to start synaptic from the menu.
  So far, I have found out that synaptic is started with pkexec.

  When I test starting
  pkexec /usr/sbin/synaptic
  in a terminal, it asks for the password in text mode.

  With another test
  pkexec --disable-internal-agent /usr/sbin/synaptic
  in the terminal, it says it has not found any authentication agent.

  I have two AMD64 PC's and a i386 laptop. The problem occurs on one of the 
PC's and the laptop.
  Comparing the /etc directory trees of the PC's showed many differences, but I 
could not find anything suspicious about the polycikit configuration.

  For the moment, using gksu instead of pkexec is a workaround.

  Thanks and Regards,
  Markus

  ProblemType: Bug
  DistroRelease: Ubuntu 12.04
  Package: policykit-1 0.104-1
  ProcVersionSignature: Ubuntu 3.2.0-22.35-generic 3.2.14
  Uname: Linux 3.2.0-22-generic x86_64
  ApportVersion: 2.0-0ubuntu4
  Architecture: amd64
  Date: Sun Apr  8 17:05:34 2012
  InstallationMedia: Xubuntu 12.04 LTS "Precise Pangolin" - Beta amd64 
(20120330)
  ProcEnviron:
   LANGUAGE=de_DE:en
   TERM=xterm
   PATH=(custom, no user)
   LANG=de_DE.UTF-8
   SHELL=/bin/bash
  SourcePackage: policykit-1
  UpgradeStatus: No upgrade log present (probably fresh install)

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