[webizen]

It is likely caused by concurrent_php module support in the new version (open_basedir is not empty). old version does not support that module and simply ignore the whole section (hence open_basedir becomes empty).

<IfModule concurrent_php.c>
        php4_admin_value open_basedir ".:/usr/lib/php:/usr/php4/lib/php:/usr/local/lib/php:/usr/local/php4/$
        php5_admin_value open_basedir ".:/usr/lib/php:/usr/local/lib/php:/tmp"
    </IfModule>
    <IfModule !concurrent_php.c>
        <IfModule mod_php4.c>
            php_admin_value open_basedir ".:/usr/lib/php:/usr/php4/lib/php:/usr/local/lib/php:/usr/local/ph$
        </IfModule>
    </IfModule>