From what it looks like to me the way your previous layout worked is in conflict with the new layout.
As the code below suggests, your sub pages should be located inside the layout/sub/ folder (this is from my website files, your might differ)
PHP:
<?php require_once 'engine/init.php'; require_once 'layout/overall/header.php';
if ($config['allowSubPages']) {
$page = (isset($_GET['page']) && !empty($_GET['page'])) ? getValue($_GET['page']) : '';
if (isset($subpages[$page]['file'])) require_once 'layout/sub/'.$subpages[$page]['file'];
else {
if (isset($subpages)) echo '<h2>Sub page not recognized.</h2><p>The sub page you requested is not recognized.</p>';
}
}
else echo '<h2>System disabled.</h2><p>The sub page system is disabled.</p>';
require_once 'layout/overall/footer.php'; ?>
And so I either suggest you to move those pages there, or, update your menu,php file to not use subpages but refer to actual php files in your website root.