When the notification emails about new comments are sent, the urls are not SEF generated.

I have fixed this modifying the file josc_com_content.class.php, in the function setRowDatas after the line:

		if (defined('_JOSC_J15')) {

add the following

			if (!$row) {

				$query = 'SELECT a.*, CASE WHEN CHAR_LENGTH(a.alias) THEN CONCAT_WS(":", a.id, a.alias) ELSE a.id END as slug, CASE WHEN CHAR_LENGTH(cc.alias) THEN CONCAT_WS(":", cc.id, cc.alias) ELSE cc.id END as catslug FROM jos_content AS a LEFT JOIN jos_categories AS cc ON cc.id = a.catid LEFT JOIN jos_sections AS s ON s.id = cc.section AND s.scope = "content" LEFT JOIN jos_users AS u ON u.id = a.created_by  WHERE a.id = '. JRequest::getInt('content_id');

				$db = JFactory::getDBO();

				$db->setQuery($query);

				$row = $db->loadObject();

			}

That is working for me, I'm not sure if it's the right one, but it could help to someone!