3.8 to 4.0 upgrade breaks file include Plugin

[EnvanoVB]

Under the plugin manager I am currently using the following:

ob_start();
   $blockHBX = true;
   include($_SERVER['DOCUMENT_ROOT'] . '/lib/header.inc.php');
   $header = ob_get_contents();
   vB_Template::preRegister('header',array('header' => $header));
ob_clean();
   $miller_forumbanner = 'projectsforum';
   $miller_noinc = true;
   include($_SERVER['DOCUMENT_ROOT'] . '/lib/footer.inc.php');
   $footer = ob_get_contents();
   vB_Template::preRegister('footer',array('footer' => $footer));
ob_end_clean();

In my 'common template' header & footer area I am using the following:

$header
$footer

Yet this is not working. it just renders it as normal PHP. Can somebody help me to get this working?