Recently i faced this problem while trying to migrate a publishing portal using stsadm backup and restore commands. I was hit by a strange problem where i wasn’t able to login into the site even with the administrative account. But i was able to login when i opened the site in Google Chrome and Firefox (?!). Finally after googling it out and going through the MSDN forums i found that it was due to some Windows Server Security patch.
You can find the fix for the issue here – http://support.microsoft.com/default.aspx/kb/896861.
The MSDN discussion link about the issue – http://social.technet.microsoft.com/Forums/en-US/sharepointadmin/thread/e044ed41-2be8-4e1c-8bcf-6460c0f0c777.