Are you setting the config files to 444 or 644? With PHP as CGI they MUST be 444.. 644 will throw that error. All the servers I've been on have been set up as php as CGI except for one. All the PHP/CGI ones required a 444, and the only way I could accomplish that was with a php script:
Code:
<?php
chmod("includes/configure.php", 0444);
chmod("admin/includes/configure.php", 0444);
?>
name it "chmod.php".. put it in the root..and hit it with your browser.. should take care of those messages. When you chmod via FTP it won't always set it to 444.. normally changes it back to 644 (at least for me.. YMMV on the ftp stuff)