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On 2 completely different machines I have the same problem after upgrading from 13.04 to 13.10: All programs/task requiering sudo permissions (software updater, starting synaptic, installing programs, shutdown) do not start / execute. No gksu (or other) window comes up. Synaptic never shows, software updater pops up with a "you are not allowed to perform this action" message.

All programs / task work when started from terminal with sudo, like "sudo synaptics" asks for my password, starts and works as expected.

I am in the admin group which is liked in sudoers config (verified with visudo and getent group admin).

Some link from GUI to gksu (or similar) is broken.

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gksu is not installed by default in 13.04 or 13.10 see this question Why is gksu no longer installed by default in 13.04?. But you can install it and its working for me in 13.10 –  Warren Hill Oct 23 '13 at 12:22
    
The problem is likely polkit. Can you edit your question and add the following: dpkg -l *policykit*. Do not use comments for adding information. –  Braiam Oct 28 '13 at 11:00

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