Why does Panels output  for some panes and  for others?
To the best of my knowledge, Panels contains no instances of &lt;section&gt;. This comes entirely from your theme.

Specifically, I believe it's from at_core/templates/panels-pane.tpl.php which contains the following:

 * Adaptivetheme variables:
 * - $is_mobile: Bool, requires the Browscap module to return TRUE for mobile
 *   devices. Use to test for a mobile context.
 * - $tag: top level wrapper element, section or div.


followed by

 &lt;&lt;?php print $tag . $attributes . $id; ?&gt;&gt;


The relevant logic appears to be

/**
 * Preprocess variables for panels_pane.tpl.php
 */
function adaptivetheme_preprocess_panels_pane(&amp;$vars) {
  // Top level wrapper
  $vars['tag'] = $vars['title'] ? 'section' : 'div';