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...
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.
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.