Ok I think I worked out why the extra queries. The moderator bar and navigation templates are not being preloaded, so I made the following change to template.php:
	
	
	
		Code:
	
	
		case 'PAGE_CONTAINER':
$template->preloadTemplate('scheduled_post_navigation_tabs');
$template->preloadTemplate('scheduled_post_moderator_bar');
break;
	 
 
I then noticed that the query for grabbing the scheduled post count is being run twice so I made the following changes:
I added to the top of template.php just above the template_hook function:
	
	
	
		Code:
	
	
		private static $countScheduleds = null;
	 
 
Then made the following change to the three instances of code which grab the count:
	
	
	
		Code:
	
	
		        $conditions = array(
           'scheduled_date' => array(">", XenForo_Application::$time)
         );
      
         if(is_null(self::$countScheduleds)) {
           self::$countScheduleds = $scheduledModel->countScheduleds($conditions);
         }
      
         $params += array(
           'viewScheduled' => $scheduledModel->viewScheduledPage(),
           'totalScheduledPosts' => self::$countScheduleds
         );
	 
 
I can send you the file to see the changes I made if it is easier, makes the add-on more query friendly 
I have not been able to figure out why the threads are not being marked as read yet though.