I would also like to add that I've been trying with the bioapi implementation - 
with the UBEK binary driver and pam_bioapi - which seems to be slightly more 
successful.
The UBEK binary driver implements a (ugly, but functional) fingerprint dialog 
(rather than relying on the user application to say "Password or swipe finger") 
- and it is my belief that it is a userspace implementation rather than one 
requiring root permissions. With this, a dialog does appear, which after a 
successful authentication, gksudo will exit as normal and the application 
requested will be executed - unlike with pam_thinkfinger currently.
Regarding this bug, it might be worth pointing out the similarity between this 
and: https://bugs.launchpad.net/bugs/15093, where I have written a length post 
regarding the problems I am experiencing with pam_bioapi, should you be 
interested.

-- 
modifying PAM configuration could break gksu
https://bugs.launchpad.net/bugs/86843
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