Does wp_nav_menu() default to ignore "manage location" sections in menus?

I am building a theme up from scratch and just got blocked by a strange issue.

When I go to the dashboard for a domain/site and create a menu for this theme, the same menu is appearing in both the header and footer. Int he dashboard the header and footer locations are appearing correctly, but when it renders, the footer menu that is selected is ignored and instead whatever the top menu is, also becomes the footer menu. Whats more once, generated I cannot select a new menu from "manage locations". The only way to get the dashboard to change the menu is to "create" a new menu, and even then the menu created fills both top header and footer location. So totally scratching my head on this, below is the entirety of the theme code. Am I missing some special hook for WPMU? Is that why the menus are acting weird? Any help is appreciated.

My header code is:

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
<title>VRLab Theme</title>
<?php wp_head(); ?>

<link rel="apple-touch-icon" href="/customIcon.png"/>

</head>

<body>

<?php wp_nav_menu(array('theme_location'**'primary')); ?>

My Footer code is this:

<footer>
<?php wp_nav_menu(array('theme_location'**'secondary')); ?>
</footer>
<?php wp_footer();  ?>
</body>
</html>

And my functions.php is simply this..

<?php

function vrlab_script_enqueue() {

	wp_enqueue_style('customstyle', get_template_directory_uri() . '/css/vrlab.css' ,array() ,'0.1a' ,'all');
	wp_enqueue_script('customjs', get_template_directory_uri() . '/js/vrlab.js' ,array() ,'0.1a' ,true);

}

add_action('wp_enqueue_scripts','vrlab_script_enqueue'); 

function vrlab_setup()  {

	add_theme_support('menus');

	register_nav_menu('primary','Primary Header Navigation');
	register_nav_menu('secondary','Footer Navigation');
}

add_action('init','vrlab_setup');

?>