I do not think this is a fault in synaptic or gnome-shell.  I can also
trigger it by simply doing the following from a command line and then
simply wait when prompted for my password:

# pkexec ls      
Error executing command as another user: Not authorized

This incident has been reported.

/var/log/auth.log then contains:

Nov 26 12:27:11 home polkit-agent-helper-1[3086]: pam_unix(polkit-1:auth): 
authentication failure; logname= uid=1000 euid=0 tty= ruser=torsten rhost=  
user=torsten
Nov 26 12:27:15 home polkitd(authority=local): Operator of 
unix-session:/org/freedesktop/ConsoleKit/Session2 FAILED to authenticate to 
gain authorization for action org.freedesktop.policykit.exec for 
unix-process:2877:136066 [zsh] (owned by unix-user:torsten)
Nov 26 12:27:15 home pkexec[3084]: torsten: Error executing command as another 
user: Not authorized [USER=root] [TTY=/dev/pts/0] [CWD=/home/torsten] 
[COMMAND=/bin/ls]

So it looks like policykit is the culprit.

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https://bugs.launchpad.net/bugs/1077546

Title:
  Gnome Shell sudo dialog said "Sorry, that didn't work. Please try
  again" when opening Synaptic

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