Most likely the problem is the uses of the virtual function for the include file:
virtual( "/WA_SecurityAssist/Helper_PHP.php" ); ?>
This actually an issue with Dreamweaver. The Virtual function is only supported on some Apache servers.
Dreamweaver will use the virtual function if you set the "Create Links Relative To:" option that is on the Local Info tab of the site Definition to "Site". Before running the Security Assist wizard, you should change that to "Document" so that Dreamweaver will use the require_once function instead.