If you find yourself able to log in under user accounts but not directly as root on one or more consoles, yet you are able to log in as a user then su - without issue, can log in over SSH or other remotely accessible services that authenticate by root account, you may have a pam_securetty misconfiguration. Check /var/log/secure:
Dec 12 08:33:20 host login: pam_securetty(login:auth): access denied: tty 'ttyS0' is not secure !
Add the missing serial interface to /etc/securetty. If using Xen, cover your bases and make sure hvc0 and xvc0 are included as well.