Last time I ran into an issue like this with Host Gator it was that the site was setup with redirects in the .htaccess that conflicted with things so that the configure.php was setup the right way and the .htaccess was forcing things to go the wrong way ...
You might look into that for giggles and grins by renaming the .htaccess to .htaccess_HIDE and then ensure that the configure.php file on the sever is correct ...
NOTE: if your configure.php file on the server is set to 444 and you are trying to FTP a new one to the server you are not going to be able to overwrite it with your new changes ...



