[Solved]
I've had this problem in Mint 13 (based on 12.04) as well but I finally tracked 
down the cause & resolved it tonight. 

I only have a single user on my machine. I noticed if I started for
example gparted manually with gksudo then I just get prompted for
password. If I start gparted from the menu it is called by pkexec
(policy kit) and I am prompted to select a user and my (only) user is
displayed twice, a duplicate entry. This is different from when clean
installed when it behaved the same as the gksudo i.e. password prompt
only. I also couldn't remember exactly what had caused this to start
happening.


I found these two files that gave me a clue: 

/etc/polkit-1/localauthority.conf.d/50-localauthority.conf
[Configuration]
AdminIdentities=unix-user:0

..and

/etc/polkit-1/localauthority.conf.d/51-ubuntu-admin.conf
[Configuration]
AdminIdentities=unix-group:sudo;unix-group:admin


User 0 is obviously root. 
I remembered when tinkering with the /etc/sudoers file I had experimented with 
group memberships. Sure enough I found my user was listed as a member of both 
the sudo and the admin groups. 

It seems polkit searches both these 'AdminIdentities' groups and since I
belonged to both groups I'm assuming that's why I was listed in the
pkexec authentication drop-down box twice.

As admin group is now deprecated (see PrecisePangolin release notes
snippet below) I simply chose to delete the admin group and logged in
again. Problem solved.

I'm sure the problem  would also have been solved by simply removing my
user from the admin group.

WARNING: You must be certain you understand the contents of /etc/sudoers
and your administrative user groups memberships before deleting groups
or removing users from such groups. Otherwise you could end up with a
system with no users allowed sudo privileges (and no root login I think
in Ubuntu systems).

In my case I think I created the admin group myself at some point as
there is a %admin group entry in /etc/sudoers by default which is
slightly different from the %sudo entry and I was curious about the
differences. So for me it was safe enough to just delete the admin
group. But if you have been upgrading from prior Ubuntu versions when
admin group WAS in use then as I've already warned you'll need to check
and be absolutely sure about the current state of how your sudo
privileges work.


https://wiki.ubuntu.com/PrecisePangolin/ReleaseNotes/UbuntuDesktop
Common Infrastructure
Up until Ubuntu 11.10, administrator access using the sudo tool was granted via 
the "admin" Unix group. In Ubuntu 12.04, administrator access will be granted 
via the "sudo" group. This makes Ubuntu more consistent with the upstream 
implementation and Debian. For compatibility purposes, the "admin" group will 
continue to provide sudo/administrator access in 12.04.


I'm not sure it's exactly a bug. Well yes it is, but an extremely low priority 
one. It doesn't happen with default install and it's only going to occur if 
some one creates an admin group and then has users belonging to both sudo and 
admin groups. 

But if someone has an excess of time and is capable of fixing this (I'm
not a coder or I would) then perhaps polkit pkexec could do a simple
check for duplicate users before displaying  the AdminIdentities drop-
down choice.

Anyway hopefully this helps anyone else searching for a fix after stumbling 
into this minor annoyance. 
G.

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https://bugs.launchpad.net/bugs/1042320

Title:
  The same user is listed multiple times in authentication dialog

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