Guillaume, I don't know what this would have to do with your upgrade, but the most common cause of mod_auth_pam failures when using pam_unix is a lack of permissions on /etc/shadow. What are the permissions on /etc/shadow on your system?
If it's not a permissions problem, we will probably need some debugging logs to make sense of this. Can you add the 'debug' option to the end of the pam_unix line in /etc/pam.d/common-auth, test, and forward the relevant lines from /var/log/debug? Thanks, -- Steve Langasek postmodern programmer
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