Disqus not showing on panel page only (panel set as homepage)
A workaround I found in this comment #5 out of the Disqus issuequeue adding disqus on the frontend. 

    function HOOK_preprocess_page(&amp;$vars) {
  if (module_exists('disqus')) {
    $identifier = $_GET['q'];
    if (strstr($identifier, 'path/to/add/comments/to')) {
      $domain = variable_get('disqus_domain', ''); // A.K.A. short name
      $url = url($_GET['q'], array('absolute' =&gt; true));
      $title = drupal_get_title();
      drupal_add_js(drupal_get_path('module', 'disqus') . '/disqus.js');
      drupal_add_js(array('disqus' =&gt; array('domain' =&gt; $domain, 'url' =&gt; $url, 'title' =&gt; $title, 'identifier' =&gt; $identifier)), 'setting'); // Add to the Drupal.settings for the script above to be able to pick it up.
      // Add the div to the page for the Disqus embed script to be able to drop in the comments code dynamically.
      $vars['page']['content']['system_main']['main']['#markup'] .= '&lt;div id="disqus_thread"&gt;&lt;/div&gt;';
    }
  }
}


Still curious about what it is in the backend that made the comment box disappear below the Panel though. I also disabled all the modules apart from the Disqus, panel en core, but still nothing.