IIRC, for most applications, the pam modules are loaded once per instance of executable linked to pam. Therefore, if you don't reload your PAM-aware executable, you will get old behavior. Additionally, you may need to check that you are properly putting new binaries in the correct place (check your specific distribution's documentation on where PAM libraries belong) and that they have the correct permissions, etc. You may also need to modify your nss related configurations (and provide a nss compliant implementation) to allow your pam module to take advantage of whatever additional accounting/authentication mechanism you're planning to use (and that will come with its own set of nightmarish requirements).
What are you specifically trying to accomplish? Some additional accounting? Authentication?