It is possible to fix the missing variables, and to add the necessary code to the header of the email to make it html based. I also modified what the %url does, in the code below it creates a link.
%urlClick here to view ticket status.%/url
CHANGE in include/class.ticket.php on about line 950
//New Ticket AutoResponse..
if($autorespond && $cfg->autoRespONNewTicket() && $dept->autoRespONNewTicket()){
$sql='SELECT ticket_autoresp_subj,ticket_autoresp_body FROM '.EMAIL_TEMPLATE_TABLE.
' WHERE cfg_id='.db_input($cfg->getId()).' AND tpl_id='.db_input($cfg->getDefaultTemplateId());
$resp=db_query($sql);
if($resp && list($subj,$body)=db_fetch_row($resp)){
$subj = str_replace("%ticket", $ticket->getExtId(),$subj);
$subj = str_replace("%name", $ticket->getName(),$subj);
$subj = str_replace("%email", $ticket->getEmail(),$subj);
$subj = str_replace("%subject", $ticket->getSubject(),$subj);
$subj = str_replace("%dept", $dept?$dept->getName():'',$subj);
$subj = str_replace("%status", $ticket->getStatus(), $subj);
$body = ''.$body;
$body = str_replace("%ticket", $ticket->getExtId(),$body);
$body = str_replace("%name", $ticket->getName(),$body);
$body = str_replace("%email", $ticket->getEmail(),$body);
$body = str_replace("%subject", $ticket->getSubject(),$body);
$body = str_replace("%dept", $dept?$dept->getName():'',$body);
$body = str_replace("%status", $ticket->getStatus(), $body);
$body = str_replace("%message",$var,$body);
$url = 'getBaseUrl().'/view.php?e='.$ticket->getEmail().'&t='.$ticket->getExtId().'">';
$body = str_replace("%url", $url, $body);
$body = str_replace("%/url", "", $body);
$body = str_replace("%signature",$dept?$dept->getSignature():'',$body);
$body .= '';
$email=$from=$fromName=null;
if(!$dept->noreplyAutoResp() && ($email=$dept->getEmail())){
$from=$email->getEmail();
$fromName=$email->getName();
//Reply separator tag.
if($cfg->stripQuotedReply() && ($tag=$cfg->getReplySeparator()))
$body ="\n$tag\n\n".$body;
}else{
$from=$cfg->getNoReplyEmail();
}
Misc:($ticket->getEmail(),$subj,$body,"KRA Support\n"."MIME-Version: 1.0\n"."Content-type: text/html; charset=iso-8859-1");
}
}