Primary Menu never receive active or active-trail classes

I checked all the bugs reported with related issues like:

• #942782: Custom menus never receive an active trail
• #1579860: No active-trail for menu items for each level greater than 2
• #1578832: [already commited but followup for CR?] <front> menu links are missing active trail classes

All the bugs is reporting that some un-expected results from the menu happens with the active and active-trail classes that must be added to the markup when the current menu link is active.

I tested all the proposed patches their and nothing fixed my bug. Firstly I was using an custom menu block generated from the menu system with no custom modules and I can't see both the active or active trail in the markup. I tried to patch it from #94278 and it didn't work with me.

So, I decided to use primary links or primary menu instead to see the active and active-trail in the markup, In my template I printed the following:

<?php if ($main_menu): ?>
          <div id="main-menu" class="navigation">
            <?php print theme('links__system_main_menu', array(
              'links' => $main_menu,
              'attributes' => array(
                'id' => 'main-menu-links',
                'class' => array('links', 'menu', 'clearfix'),
              ),
              'heading' => array(
                'text' => t('Main menu'),
                'level' => 'h2',
                'class' => array('element-invisible'),
              ),
            )); ?>
          </div> <!-- /#main-menu -->
        <?php endif; ?>

In the theme.info file I added:
features[] = main_menu

In template.php I added the following to add the child-menues to the menu array:

function themeName_links($variables) { 
  if (array_key_exists('id', $variables['attributes']) && $variables['attributes']['id'] == 'main-menu-links') { 
      $pid = variable_get('menu_main_links_source', 'main-menu'); 
    $tree = menu_tree($pid); 
    return drupal_render($tree); 
  } 
  return theme_links($variables); 
}

Everything is working and the menu appears with the child menues, But I can't find the active or active-trail classes in any link in the menu.

I only use Special menu items custom module to be able to make some links without urls in the menu. Disabling this module didn't help too.

Direct link to the site Human Nature Blog the menu on the left sidebar is the primary menu.

I am ready to help and provide any further information.