Fedora 12 uses pam module called pam_succeed_if.so. This module is designed to succeed or fail authentication based on characterstics of the account of the authenticated user. Default configuration of this module blocks root login using GUI.
Login as Normal User.
Open the terminal and use vim or gedit to open the /etc/pam.d/gdm
su -c "vim /etc/pam.d/gdm"
Comment the following line
'auth required pam_succeed_if.so user !=root quiet'
# auth required pam_succeed_if.so user != root quiet
Do the same for "/etc/pam.d/gdm-password
Save the file and logout from GUI. Now you can login as root :)
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