Change the code in the modulehelper.php file

/var/www/plugins/system/jat3/jat3/core/joomla/modulehelper.php 

The problem code is on line 292

$Itemid = JRequest::getInt('Itemid');
$app = JFactory::getApplication();
$user = JFactory::getUser();
$groups = implode(',', $user->getAuthorisedViewLevels());
$db = JFactory::getDbo();
jimport("joomla.database.databasequery");

// comment out the line below
// $query = new JDatabaseQuery;

// add the line below
$query = $db->getQuery(true);

$query->select('id, title, module, position, content, showtitle, params, mm.menuid');
$query->from('#__modules AS m');
$query->join('LEFT','#__modules_menu AS mm ON mm.moduleid = m.id');
$query->where('m.published = 1');

This seems to have sorted the problem