Main menu doesn't take "show as expanded" option into account for menu items

Hello,

We have a theme as a subtheme of the Bootstrap theme. After upgrading from 3.14 to 3.16 we noticed that menu option "show as expanded" doesn't work anymore: items are always expanded, whatever the option selected for them. I tracked the problem and it is due to the difference in page.vars.php. In version 7.15 it is

// Primary nav.
  $variables['primary_nav'] = FALSE;
  if ($variables['main_menu']) {
    // Build links.
    $variables['primary_nav'] = menu_tree(variable_get('menu_main_links_source', 'main-menu'));

whereas in 3.16 it is

// Primary nav.
  $variables['primary_nav'] = FALSE;
  if ($variables['main_menu']) {
    // Load the tree
    $tree = menu_tree_all_data(variable_get('menu_main_links_source', 'main-menu'));

    // Localize the tree.
    if ($i18n) {
      $tree = i18n_menu_localize_tree($tree);
    }

    // Build links.
    $variables['primary_nav'] = menu_tree_output($tree);

I'm not a developer so I don't know how to solve this issue, except using the code from 3.15 in 3.16