Ok Devil...when alot of php pages render, they include other pages. So basically your php page will be alot of if else statements that include different things and set variables along the way, so you are not going to see a whole lot of HTML markup. Basically what your phpNuke template is doing is including three files (and also a footer, but I am ignoring that), two of which have a head defined in them. This is poor HTML and just might be causing some problems...not your fault. There are three includes I can see,
include("themes/$ThemeSel/module.php");
include($modpath);
include("header.php");
The variables are the strings that start with $, so they are dynamic. You need to figure out what themes you are using and find the php files that are being included, as well as whats in the header.php file, and see where your duplicate heads are coming from.
And the links to the quick references are at
http://milonic.com and they are located under the menu item "DHTML Menu"...can't miss 'em.