I am experiencing a similar bug: this time using pam_bioapi (to support 
fingerprint readers), version 0.4.0.
The problem I am having is that gksudo does not pop up to ask for a password 
once the fingerprint dialog is aborted, as it would be expected to do.
My common-auth is as follows:
auth    sufficient      pam_bioapi.so {5550454b-2054-464d-2f45-535320425350} 
/etc/bioapi/pam/biodata.db :0

auth       required     pam_unix.so nullok_secure
gdm, and console-run sudo perform as expected - cancelling the fingerprint 
dialog and it will ask for a password. However, running gksudo from console 
results in:
# sudo -l
# gksudo gedit
<fingerprint dialog pops up - after exiting that>
GNOME_SUDO_PASS
at which point it echoes any characters I type at it (meaning that it's not 
asking for a password), including new line characters. The only way to abort 
this is to press Ctrl+C.
Note also that the screen is not blanked during the fingerprint dialog 
(separate bug?)
Running gksudo from a launcher has the same effect - but obviously no console 
output.
Does anyone know what GNOME_SUDO_PASS means? I've asked the google oracle, but 
that hasn't got me anywhere. 
I can confirm that gksudo works perfectly well without the pam_bioapi line, and 
it also works if I make it ask for the password first, by changing common-auth 
to:
auth    sufficient      pam_unix.so nullok_secure


auth    sufficient      pam_bioapi.so {5550454b-2054-464d-2f45-535320425350} 
/etc/bioapi/pam/biodata.db :0

auth    required        pam_deny.so
gksudo does blank the screen and the password dialog appears, and pressing 
enter results in it unblanking and the fingerprint dialog appearing - this is 
my current solution, but far from ideal as I would like the password to back 
the fingerprinting.
It is also worth mentioning that this is also the case with pam_thinkfinger (an 
alternative fingerprinting "driver") which does not implement a separate 
fingerprinting dialog - gksudo does not appear at all, and after a successful 
fingerprint read gksudo does not exit - and a killall is required to bring the 
authenticating application up - though this also may be a error with 
pam_thinkfinger (version tested: 0.3.0).
All in all, I think we can conclude that gksudo (which from what I understand, 
is simply a wrapper for the console based sudo) does not support external pam 
modules very well?

-- 
gksudo fails if using libpam-krb5 for password auth
https://bugs.launchpad.net/bugs/15093
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