the menu is generated by the webassist/plugins/main_menu/menu.php file.
you will need to remove the custom menu section:
<li class="parent top"><span><a href="../../../page.php?Custom Menu=1">
<?php echo WA_getCMSContent($database_PowerStoreConnection, $PowerStoreConnection, 'Custom Menu', 'Menu Label', true); ?></a></span>
<ul class="level-1">
<?php
echo($WACustomPages->Body);
?>
</ul>
</li>