I have the same problem using fprint (http://reactivated.net/fprint) on Hardy 
Heron RC.
        
Pending a solution, I restored the original common-auth and use the login 
through fingerprint reader only for the GDM (no sudo or gksu).

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