net-mail/checkpassword-pam-0.99 installs /usr/bin/checkpassword-pam with the wrong permissions. In order to check a password against the /etc/shadow files (using the PAM libraries) for correctness it must be run as root or installed SUID root. Simple fix:
chmod ug+s /usr/bin/checkpassword-pam
This bug is still open as well. Somehow I just ran into this as well, on a system that I had been updating in the past few months, just not last couple of weeks. This needs to be addressed ASAP, thanks!
*** This bug has been marked as a duplicate of bug 142000 ***