Bootstrap subtheme - theme_menu_link(array $variables) not reacting
I maintain a Bootstrap subtheme that I use for most of my projects and I override theme_menu_link() in my subtheme using the same method with no problem:

/**
 * Overrides bootstrap_menu_link().
 *
 * Resets theme_menu_link() to the default that ships with Drupal. Bootstrap
 * attempts to make every menu with children into a dropdown menu. Remove this
 * function if you want drop down links.
 */
function bootstrap_ignitor_menu_link(array $variables) {
  $element = $variables['element'];
  $sub_menu = '';
  if ($element['#below']) {
    $sub_menu = drupal_render($element['#below']);
  }
  $output = l($element['#title'], $element['#href'], $element['#localized_options']);
  return '&lt;li' . drupal_attributes($element['#attributes']) . '&gt;' . $output . $sub_menu . "&lt;/li&gt;\n";
}


You must have a problem somewhere else.