After upgrading to sys-libs/pam-1.0.1 the following appears in logs on every login: pam_tally(login:account): option deny=0 allowed in auth phase only pam_tally(login:account): unknown option: no_magic_root These deprecated strings should be removed from the config files as part of the ebuild.
Did you update the configuration files with the ones provided by pambase? Because the default configuration does not use no_magic_root nor deny=0 for pam_tally. Updating custom pam.d files is not something that ebuild should do, as they could mess the system login up a lot.
