php cannot locate plugin path

I have added header and footer plugs to a theme though I notice an abnormality when the paths are generated (see below)

<?php require_once('file:///C|/Users/Timothy/Documents/uwhosting.com/webassist/framework/framework.php'); ?>
<?php require_once('file:///C|/Users/Timothy/Documents/uwhosting.com/webassist/framework/library.php'); ?>
<?php
if("" == ""){
$WA_header_nav_1398215934234 = new WA_Include("file:///C|/Users/Timothy/Documents/uwhosting.com/Modules/header-nav.php");
require($WA_header_nav_1398215934234->BaseName);
$WA_header_nav_1398215934234->Initialize(true);
}

if("" == ""){
$WA_footer_nav_1398264335704 = new WA_Include("../Modules/footer-nav.php");
require($WA_footer_nav_1398264335704->BaseName);
$WA_footer_nav_1398264335704->Initialize(true);
}
?>

once saved the paths locate the files properly except for the footer nav which stays

Header Nav
$WA_header_nav_1398215934234 = new WA_Include("Modules/header-nav.php");

Footer Nav
$WA_footer_nav_1398264335704 = new WA_Include("../Modules/footer-nav.php");

If I remove the "../" the file is found and works properly

the template has defined the following for these items

<?php
if("" == ""){
$WA_header_nav_1398215934234 = new WA_Include("../Modules/header-nav.php");
require($WA_header_nav_1398215934234->BaseName);
$WA_header_nav_1398215934234->Initialize(true);
}

if("" == ""){
$WA_footer_nav_1398264335704 = new WA_Include("../Modules/footer-nav.php");
require($WA_footer_nav_1398264335704->BaseName);
$WA_footer_nav_1398264335704->Initialize(true);
}
?>

as editing this path is not supported by dreamweaver templates (any updates will cause the paths to revert.

Thank you for your assistance.

Best Regards,

Tim