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So, basically what's in the tittle. I can execute any installed program with both Synapse and Unity, but if it requires SUDO authentication (like Synaptic, Y-PPA manager) it doesn't launch.

It's clearly a problem with policykit or something like that. I'm not an expert and so I cannot backtrack or troubleshoot the problem by myself...

Thanks!


First Edit

Just some more details: - Launching said programs in terminal with $sudo works fine. - Launching said programs in terminal with $gksudo also works fine, the password popup appears.


Second Edit

Upon request from @steeldriver in the comment section

$ synaptic-pkexec
==== AUTHENTICATING FOR com.ubuntu.pkexec.synaptic ===
Authentication is required to run the Synaptic Package Manager
Authenticating as: [my name] ([my username])
Password: 
polkit-agent-helper-1: error response to PolicyKit daemon: GDBus.Error:org.freedesktop.PolicyKit1.Error.Failed: No session for cookie
==== AUTHENTICATION FAILED ===
Error executing command as another user: Not authorized

This incident has been reported.
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    Are there any error messages that might be useful if you run something like synaptic-pkexec or pkexec synaptic in a terminal? – steeldriver Jul 5 '16 at 10:45
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    OK thanks - and just to confirm, you are running this locally (not for example remotely via xrdp or vnc)? – steeldriver Jul 5 '16 at 11:43
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    Is the authentication agent running? You can check with (for example) ps -ef | grep [p]olkit – steeldriver Jul 5 '16 at 12:01
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    You should also see something like /usr/lib/policykit-1-gnome/polkit-gnome-authentication-agent-1 I think – steeldriver Jul 5 '16 at 12:24
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    It should be started automatically by the /etc/xdg/autostart/polkit-gnome-authentication-agent-1.desktop file - you will need to figure out why that's not happening. Sorry I need to step away now - good luck. – steeldriver Jul 5 '16 at 12:38
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Maybe authentication-agent is not running. Run the following command to run the agent

/usr/lib/policykit-1-gnome/polkit-gnome-authentication-agent-1

If it works then run that on startup.

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