Dreamweaver .htaccess prepend

In my .htaccess file, I'm using such things as the following:
php_value    include_path            ".:/usr/local/php-5.2.6-1/share/pear:/nfs/c03/h05/mnt/foo/domains/bar/html"
php_value    doc_root                "/nfs/c03/h05/mnt/foo/domains/bar/html"
php_value    open_basedir            "/nfs/c03/h05/mnt/foo/"

php_value    auto_prepend_file        "modules/template/prepend.php"

How can I get Dreamweaver to read the .htaccess file so that it can find all the related files properly?  For example, most of my site's PHP files include modules/template/header.php but because Dreamweaver isn't detecting the include_path, it can't find the header file.  As a result of that, the CSS files are automatically loaded.

Thanks,

LSTC Webmaster