I've seen the same wrong behavior with pam_pkcs11 module.

Even changing the PIN prompt to say "Password:", gksu does not work
correctly, due to timeout.

My smart card needs about 30 - 60 seconds to handshake, bug gksudo only waits a 
password prompt for about 5 seconds.
So, when pam_pkcs11 module prompts for a password, gksu wrongly thinks no 
password was needed and sudo did success.

I thing libgksu needs a major refactor to properly handle those password
prompts, and not to relay on a sudo pipe.

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gksu not prompting when pam_musclecard in use
https://bugs.launchpad.net/bugs/52018
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