Got same issue after an upgrade from Ubuntu 14.04 to 16.04 and the
following actions solved the problem :

sudo pam-auth-update --force
sudo vi/etc/pam.d/lightdm

=> add following lines at the end : 
        session required pam_loginuid.so
        session required pam_systemd.so

sudo reboot

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You received this bug notification because you are a member of Ubuntu
Touch seeded packages, which is subscribed to lightdm in Ubuntu.
https://bugs.launchpad.net/bugs/1240336

Title:
  After release upgrade, the user looses permissions for several basic
  actions in the system

Status in gdm package in Ubuntu:
  Triaged
Status in lightdm package in Ubuntu:
  Triaged
Status in lxdm package in Ubuntu:
  Triaged
Status in policykit-desktop-privileges package in Ubuntu:
  Triaged

Bug description:
  HOW TO REPRODUCE:
  - Upgrade Ubuntu to the next release.

  RESULT:
  - The user looses permissions for several basic actions in the system.

  ProblemType: Bug
  DistroRelease: Ubuntu 13.10
  Package: policykit-desktop-privileges 0.16
  ProcVersionSignature: Ubuntu 3.11.0-12.19-generic 3.11.3
  Uname: Linux 3.11.0-12-generic x86_64
  ApportVersion: 2.12.5-0ubuntu2
  Architecture: amd64
  Date: Tue Oct 15 20:20:55 2013
  InstallationDate: Installed on 2013-10-09 (7 days ago)
  InstallationMedia: Ubuntu 13.10 "Saucy Salamander" - Beta amd64 (20131008)
  MarkForUpload: True
  PackageArchitecture: all
  ProcEnviron:
   LANGUAGE=en_US
   TERM=xterm
   PATH=(custom, no user)
   LANG=en_US.UTF-8
   SHELL=/bin/bash
  SourcePackage: policykit-desktop-privileges
  UpgradeStatus: No upgrade log present (probably fresh install)

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