I'm not sure what timer you are using, but make sure you have GD library installed on the server. That may be the reason why the timer is not showing.
I believe it is not about that. because as of now i have 4 auroras hosted under me but they don't face the same issue. 
source/clicking/timer.php is for the actual timer so take a look here
good luck
Already checked.
this is the code.
I didn't find unusual, 
<?
if(!IN_CLICKING) exit;
$referringurl=parse_url($HTTP_REFERER);
$selfurl=parse_url($_SERVER['PHP_SELF']);
if (!($referringurl['path'] == $selfurl['path'] && $referringurl['host'] == $_SERVER['HTTP_HOST'])) {
logError("Failed referring host check while clicking: {$HTTP_REFERER}");
error("There was an error validating your session");
}
if($id != -1) {
if(true) { //TODO setup admin setting for showing banner
$banner=$Db1->query_first("SELECT * FROM banners WHERE credits>=1 order by rand() limit 1");
if(isset($banner[id])) $Db1->query("UPDATE banners SET credits=credits-1, views=views+1 WHERE id='{$banner[id]}'");
}
$key=$Db1->querySingle("SELECT val FROM click_sessions WHERE dsub='{$pretime}' and username='{$username}' and type='{$type}' ","val");
srand ((float) microtime() * 10000000);
$buttons = array ("1", "2", "3", "4", "5", "6", "7", "8", "9");
$rand_keys = array_rand ($buttons, 4);
$key = $buttons[$rand_keys[$key]];
for($x=0; $x<4; $x++) { $buttonlist.="<li><a href=\"#\" onclick=\"next({$x})\" id=\"button{$x}\"><img src=\"clickimages/".$buttons[$rand_keys[$x]].".gif\" alt=\"Button\" /></a></li>\n"; }
$t = $Db1->query_first("SELECT ".(($type=="ce" || $type=="ptre")?"":"timed,")." target FROM ".$adTables[$type]." WHERE id='{$id}'");
if($type=="ce") $timer=$settings['ce_time'];
elseif($type=="ptre") $timer=$settings['ptr_time'];
else $timer=$t['timed'];
$target=$t['target'];
}
?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="content-type" content="application/xhtml+xml; charset=UTF-8" />
<title><?=$settings['site_title'];?></title>
<link href="templates/<?=$settings['template'];?>/timer.css?" rel="stylesheet" type="text/css" />
<script type="text/javascript">
var id="<?=$id;?>";
var url_variables="<?=$url_variables;?>";
var timer=<? echo ($timer+1); ?>;
var type="<?=$type;?>";
var key="<?=$key;?>";
var pretime="<?=$pretime;?>";
</script>
<script type="text/javascript" src="./includes/ajax/jquery.js"></script>
<script type="text/javascript" src="./source/clicking/timer.js"></script>
</head>
<body>
<div id="banner"><a href="bannerclick.php?id=<?=$banner[id];?>" target="_blank"><img src="<?=$banner[banner];?>" alt="Banner Advertisement" /></a></div>
<div id="timer">Loading</div>
<div id="buttons"><ul><?=$buttonlist;?></ul></div>
<div id="menu">
<li><a href="<?=$target;?>" target="_blank">New Window</a></li>
<li><a href="#" onClick="reportAd()">Report</a></li>
<li>Earned Today: $<?=$thismemberinfo['earned_today'];?></li><li>Click Exchange Clicks : <?=$thismemberinfo['xclicked_today'];?>
<? if(!$LOGGED_IN && !$type == "ptre") { ?>
<li><a href="index.php?view=join&<? echo $url_variables; ?>"><span><span>Register</span></span></a></li>
<li><a href="index.php?view=login&<? echo $url_variables; ?>"><span><span>Login</span></span></a></li>
<? } ?>
</div>
<div id="logo"></div>
</body>
</html>
Also good to check your source/clicking/timer.js is ok
function reportAd() {
window.open("gpt.php?v=report&id="+id+"&type="+type+"&"+url_variables+"","","width=500,height=400,status=1")
}
function next(num) {
if(timer == 0) {parent.location.href='gpt.php?v=verify&buttonClicked='+num+'&id='+id+'&type='+type+'&pretime='+pretime+'&'+url_variables+'';}
else { alert("You must wait for the counter to reach 0"); }
}
function adTimer() {
timer--;
if(timer == 0) {
var show="Click "+key;
$("#buttons").fadeIn();
}
else {
var show="Wait: "+timer;
setTimeout(adTimer, 1000);
}
$("#timer").html(show);
}
$(document).ready(function() {
if(id != -1) adTimer();
else $("#timer").html("Cheat Check");
});
everything seems fine. 