Again I never used ubb6 but can only assume the issues are similar with ubb7
I can only assume that the config.inc.php file got wiped.
which is a known bug.
As far as the header html that is normally saved in header.php a separate file but still in the includes folder.
I would first double check the permissions for that folder and files within. and make sure you are the owner of the folder and files.
You can check both items with a ftp program.