Show menu link descriptions for a custom navigation menu
Here are two things that may help you get this going:


It looks like you're calling the theme_links() rather than the theme_link() function in your page.tpl.php file, so make sure that the call and theme function implementation match.
You could add additional information to your links when you theme them to distinguish them from other links.  For example, notice how I'm adding an id in the 'attributes' section below, so I can check for it later, in my theme_links implementation


Does that help?

 print theme('links', array(
  'links' =&gt; $secondary_menu,
  'attributes' =&gt; array(
    'id' =&gt; 'secondary-menu',
    'class' =&gt; array('links', 'inline', 'clearfix'),
  ),
  'heading' =&gt; array(
    'text' =&gt; $secondary_menu_heading,
    'level' =&gt; 'h2',
    'class' =&gt; array('element-invisible'),
  ),
));