boyvanamstel

This fixed it for me: just add ‘nav_menu_item’ to the post types in the filter method provided above.

add_filter('pre_get_posts', 'query_post_type');
function query_post_type($query) {
  if(is_category() || is_tag()) {
    $post_type = get_query_var('post_type');
	if($post_type)
	    $post_type = $post_type;
	else
	    $post_type = array('nav_menu_item','post','articles');
    $query->set('post_type',$post_type);
	return $query;
    }
}

Exact method I use: https://gist.github.com/1055880

EDIT: I meant ‘nav_menu_item’

Thanks Kevin, for further investigating the issue.

I’ll try the workaround :).