I don't know if it has been covered before, but an alternative to using cPanel or FTP to try to change file permissions is using PHP to do it... Maybe it could be part of the install script; "Set permissions on configuration files?"
Code:
<?php
/*
Changing file rights with php, an alternative to changing rights with cPanel/ftp/shell.
Pop this in a file named rights.php in you root directory for Zen-Cart, then execute it:
http://{www.mydomain.com/somepath}/rights.php
Be sure to delete the file when you're done!
*/
chmod("admin/includes/configure.php", 0444);
chmod("includes/configure.php", 0444);
echo "Rights changed!<br><b>Delete this file! (" . $_SERVER["SCRIPT_NAME"] . ")</b>";
?>