I can see very similar issue in unlocking of gdm locked screen. 
That was annoying more than launching synaptic, because I could start synaptic by gksudo or sudo synaptic on command line or in ALT+F2 dialog in Gnome-shell.

Not sure what it tries to get, but from auth.log 

Dec  7 12:02:28 localhost gdm-password][7244]: pam_succeed_if(gdm-password:auth): requirement "user ingroup nopasswdlogin" not met by user "mnovotny"
Dec  7 12:02:30 localhost gdm-password][7244]: gkr-pam: unlocked login keyring
Dec  7 12:05:01 localhost CRON[7519]: pam_unix(cron:session): session opened for user root by (uid=0)
Dec  7 12:05:01 localhost CRON[7519]: pam_unix(cron:session): session closed for user root
Dec  7 12:06:20 localhost sshd[1316]: Server listening on 0.0.0.0 port 22.
Dec  7 12:06:20 localhost sshd[1316]: Server listening on :: port 22.
Dec  7 12:06:27 localhost dbus[1563]: [system] Rejected send message, 1 matched rules; type="method_call", sender=":1.5" (uid=0 pid=1584 comm="gdm ") interface="org.freedesktop.DBus.Properties" member="GetAll" error name="(unset)" requested_reply="0" destination=":1.8" (uid=0 pid=1644 comm="/usr/lib/gdm/gdm-simple-slave --display-id /org/gn")
Dec  7 12:06:40 localhost dbus[1563]: [system] Rejected send message, 1 matched rules; type="method_call", sender=":1.5" (uid=0 pid=1584 comm="gdm ") interface="org.freedesktop.DBus.Properties" member="GetAll" error name="(unset)" requested_reply="0" destination=":1.19" (uid=0 pid=2399 comm="/usr/lib/gdm/gdm-simple-slave --display-id /org/gn")
Dec  7 12:06:43 localhost gdm-launch-environment][2415]: pam_unix(gdm-launch-environment:session): session opened for user gdm by (uid=0)
Dec  7 12:06:43 localhost gdm-launch-environment][2415]: pam_ck_connector(gdm-launch-environment:session): nox11 mode, ignoring PAM_TTY :1
Dec  7 12:06:46 localhost su[2632]: Successful su for root by root
Dec  7 12:06:46 localhost su[2632]: + ??? root:root
Dec  7 12:06:46 localhost su[2632]: pam_unix(su:session): session opened for user root by (uid=0)
Dec  7 12:06:46 localhost su[2632]: pam_unix(su:session): session closed for user root
Dec  7 12:06:54 localhost dbus[1563]: [system] Rejected send message, 2 matched rules; type="method_call", sender=":1.38" (uid=124 pid=2790 comm="gnome-shell --mode=gdm ") interface="org.freedesktop.DBus.Properties" member="GetAll" error name="(unset)" requested_reply="0" destination=":1.24" (uid=0 pid=2422 comm="/usr/sbin/console-kit-daemon --no-daemon ")
Dec  7 12:06:54 localhost dbus[1563]: [system] Rejected send message, 2 matched rules; type="method_call", sender=":1.38" (uid=124 pid=2790 comm="gnome-shell --mode=gdm ") interface="org.freedesktop.DBus.Properties" member="GetAll" error name="(unset)" requested_reply="0" destination=":1.24" (uid=0 pid=2422 comm="/usr/sbin/console-kit-daemon --no-daemon ")
Dec  7 12:06:54 localhost polkitd(authority=local): Registered Authentication Agent for unix-session:/org/freedesktop/ConsoleKit/Session1 (system bus name :1.38 [gnome-shell --mode=gdm], object path /org/freedesktop/PolicyKit1/AuthenticationAgent, locale en_US.UTF-8)
Dec  7 12:06:54 localhost dbus[1563]: [system] Rejected send message, 2 matched rules; type="method_call", sender=":1.38" (uid=124 pid=2790 comm="gnome-shell --mode=gdm ") interface="org.freedesktop.DBus.Properties" member="GetAll" error name="(unset)" requested_reply="0" destination=":1.24" (uid=0 pid=2422 comm="/usr/sbin/console-kit-daemon --no-daemon ")
Dec  7 12:07:50  dbus[1563]: last message repeated 4 times
Dec  7 12:07:50 localhost gdm-password][2867]: pam_succeed_if(gdm-password:auth): requirement "user ingroup nopasswdlogin" not met by user "mnovotny"
Dec  7 12:07:55 localhost gdm-password][2867]: pam_unix(gdm-password:session): session opened for user mnovotny by (uid=0)
Dec  7 12:07:55 localhost gdm-password][2867]: pam_ck_connector(gdm-password:session): nox11 mode, ignoring PAM_TTY :1
Dec  7 12:07:55 localhost gdm-launch-environment][2415]: pam_unix(gdm-launch-environment:session): session closed for user gdm
Dec  7 12:07:55 localhost polkitd(authority=local): Unregistered Authentication Agent for unix-session:/org/freedesktop/ConsoleKit/Session1 (system bus name :1.38, object path /org/freedesktop/PolicyKit1/AuthenticationAgent, locale en_US.UTF-8) (disconnected from bus)
Dec  7 12:07:57 localhost gnome-keyring-daemon[2933]: Gkm: using old keyring directory: /home/mnovotny/.gnome2/keyrings
Dec  7 12:07:57 localhost gnome-keyring-daemon[2933]: Gkm: using old keyring directory: /home/mnovotny/.gnome2/keyrings
Dec  7 12:08:00 localhost sudo: mnovotny : TTY=unknown ; PWD=/home/mnovotny ; USER=root ; COMMAND=/usr/lib/jupiter/scripts/vga-out mon silent
Dec  7 12:08:00 localhost sudo: mnovotny : TTY=unknown ; PWD=/home/mnovotny ; USER=root ; COMMAND=/usr/lib/jupiter/scripts/vga-out restore silent
Dec  7 12:08:00 localhost sudo: mnovotny : TTY=unknown ; PWD=/home/mnovotny ; USER=root ; COMMAND=/usr/lib/jupiter/scripts/bluetooth restore
Dec  7 12:08:00 localhost sudo: pam_unix(sudo:session): session opened for user root by (uid=0)
Dec  7 12:08:00 localhost sudo: pam_unix(sudo:session): session opened for user root by (uid=0)
Dec  7 12:08:00 localhost sudo: mnovotny : TTY=unknown ; PWD=/home/mnovotny ; USER=root ; COMMAND=/usr/lib/jupiter/scripts/cpu-control restore
Dec  7 12:08:00 localhost sudo: pam_unix(sudo:session): session opened for user root by (uid=0)
Dec  7 12:08:00 localhost sudo: pam_unix(sudo:session): session opened for user root by (uid=0)
Dec  7 12:08:00 localhost sudo: pam_unix(sudo:session): session closed for user root
Dec  7 12:08:06  sudo: last message repeated 3 times
Dec  7 12:08:06 localhost dbus[1563]: [system] Rejected send message, 2 matched rules; type="method_call", sender=":1.53" (uid=1000 pid=3068 comm="gnome-shell --sm-client-id 10f30854e7c9fc0eed13530") interface="org.freedesktop.DBus.Properties" member="GetAll" error name="(unset)" requested_reply="0" destination=":1.24" (uid=0 pid=2422 comm="/usr/sbin/console-kit-daemon --no-daemon ")
Dec  7 12:08:06 localhost dbus[1563]: [system] Rejected send message, 2 matched rules; type="method_call", sender=":1.53" (uid=1000 pid=3068 comm="gnome-shell --sm-client-id 10f30854e7c9fc0eed13530") interface="org.freedesktop.DBus.Properties" member="GetAll" error name="(unset)" requested_reply="0" destination=":1.24" (uid=0 pid=2422 comm="/usr/sbin/console-kit-daemon --no-daemon ")
Dec  7 12:08:11 localhost sudo: mnovotny : TTY=unknown ; PWD=/home/mnovotny ; USER=root ; COMMAND=/usr/lib/jupiter/scripts/cpu-control vendor
Dec  7 12:08:11 localhost sudo: pam_unix(sudo:session): session opened for user root by (uid=0)
Dec  7 12:08:11 localhost sudo: pam_unix(sudo:session): session closed for user root
Dec  7 12:08:15 localhost dbus[1563]: [system] Rejected send message, 2 matched rules; type="method_call", sender=":1.53" (uid=1000 pid=3068 comm="gnome-shell --sm-client-id 10f30854e7c9fc0eed13530") interface="org.freedesktop.DBus.Properties" member="GetAll" error name="(unset)" requested_reply="0" destination=":1.24" (uid=0 pid=2422 comm="/usr/sbin/console-kit-daemon --no-daemon ")
Dec  7 12:08:16 localhost polkitd(authority=local): Registered Authentication Agent for unix-session:/org/freedesktop/ConsoleKit/Session3 (system bus name :1.53 [gnome-shell --sm-client-id 10f30854e7c9fc0eed135307739419945200000038490000], object path /org/freedesktop/PolicyKit1/AuthenticationAgent, locale en_US.UTF-8)
Dec  7 12:08:39 localhost gnome-keyring-daemon[2933]: keyring alias directory: /home/mnovotny/.gnome2/keyrings
Dec  7 12:08:44 localhost dbus[1563]: [system] Rejected send message, 2 matched rules; type="method_call", sender=":1.53" (uid=1000 pid=3068 comm="gnome-shell --sm-client-id 10f30854e7c9fc0eed13530") interface="org.freedesktop.DBus.Properties" member="GetAll" error name="(unset)" requested_reply="0" destination=":1.24" (uid=0 pid=2422 comm="/usr/sbin/console-kit-daemon --no-daemon ")
Dec  7 12:09:50  dbus[1563]: last message repeated 3 times
Dec  7 12:15:01 localhost CRON[3962]: pam_unix(cron:session): session opened for user root by (uid=0)
Dec  7 12:15:01 localhost CRON[3962]: pam_unix(cron:session): session closed for user root
Dec  7 12:17:01 localhost CRON[4001]: pam_unix(cron:session): session opened for user root by (uid=0)
Dec  7 12:17:01 localhost CRON[4001]: pam_unix(cron:session): session closed for user root
Dec  7 12:20:43 localhost dbus[1308]: [system] Rejected send message, 1 matched rules; type="method_call", sender=":1.11" (uid=0 pid=1528 comm="gdm ") interface="org.freedesktop.DBus.Properties" member="GetAll" error name="(unset)" requested_reply="0" destination=":1.13" (uid=0 pid=1588 comm="/usr/lib/gdm/gdm-simple-slave --display-id /org/gn")
Dec  7 12:20:46 localhost gdm-launch-environment][2140]: pam_unix(gdm-launch-environment:session): session opened for user gdm by (uid=0)
Dec  7 12:20:46 localhost gdm-launch-environment][2140]: pam_ck_connector(gdm-launch-environment:session): nox11 mode, ignoring PAM_TTY :0
Dec  7 12:20:50 localhost dbus[1308]: [system] Rejected send message, 2 matched rules; type="method_call", sender=":1.31" (uid=124 pid=2500 comm="gnome-shell --mode=gdm ") interface="org.freedesktop.DBus.Properties" member="GetAll" error name="(unset)" requested_reply="0" destination=":1.18" (uid=0 pid=2147 comm="/usr/sbin/console-kit-daemon --no-daemon ")
Dec  7 12:20:50 localhost dbus[1308]: [system] Rejected send message, 2 matched rules; type="method_call", sender=":1.31" (uid=124 pid=2500 comm="gnome-shell --mode=gdm ") interface="org.freedesktop.DBus.Properties" member="GetAll" error name="(unset)" requested_reply="0" destination=":1.18" (uid=0 pid=2147 comm="/usr/sbin/console-kit-daemon --no-daemon ")
Dec  7 12:20:50 localhost polkitd(authority=local): Registered Authentication Agent for unix-session:/org/freedesktop/ConsoleKit/Session1 (system bus name :1.31 [gnome-shell --mode=gdm], object path /org/freedesktop/PolicyKit1/AuthenticationAgent, locale en_US.UTF-8)
Dec  7 12:20:50 localhost dbus[1308]: [system] Rejected send message, 2 matched rules; type="method_call", sender=":1.31" (uid=124 pid=2500 comm="gnome-shell --mode=gdm ") interface="org.freedesktop.DBus.Properties" member="GetAll" error name="(unset)" requested_reply="0" destination=":1.18" (uid=0 pid=2147 comm="/usr/sbin/console-kit-daemon --no-daemon ")
Dec  7 12:20:55  dbus[1308]: last message repeated 4 times
Dec  7 12:20:55 localhost gdm-password][2743]: pam_succeed_if(gdm-password:auth): requirement "user ingroup nopasswdlogin" not met by user "mnovotny"
Dec  7 12:20:58 localhost gdm-password][2743]: pam_unix(gdm-password:session): session opened for user mnovotny by (uid=0)
Dec  7 12:20:58 localhost gdm-password][2743]: pam_ck_connector(gdm-password:session): nox11 mode, ignoring PAM_TTY :0
Dec  7 12:20:58 localhost dbus[1308]: [system] Rejected send message, 2 matched rules; type="method_call", sender=":1.31" (uid=124 pid=2500 comm="gnome-shell --mode=gdm ") interface="org.freedesktop.DBus.Properties" member="GetAll" error name="(unset)" requested_reply="0" destination=":1.18" (uid=0 pid=2147 comm="/usr/sbin/console-kit-daemon --no-daemon ")
Dec  7 12:20:58 localhost dbus[1308]: [system] Rejected send message, 2 matched rules; type="method_call", sender=":1.31" (uid=124 pid=2500 comm="gnome-shell --mode=gdm ") interface="org.freedesktop.DBus.Properties" member="GetAll" error name="(unset)" requested_reply="0" destination=":1.18" (uid=0 pid=2147 comm="/usr/sbin/console-kit-daemon --no-daemon ")