I'm not sure how your popup is set up and it is actually something that isn't supported since it requires custom coding, however it could have something to do with the add to cart button forwarding to another page that is causing the window to close again. Maybe if you posted a link to the page, someone will have a better idea and can help you out. 
Hi Jimmy.
I had the same thought with regards to the page forwarding but even after removing forwarding links, it doesn't seem to work properly. I thought that it maybe a conflict with the mini cart so created a new blank page, but the css window only shows for a second and then closes.
I have a local server set up so can't provide a link to the page, but here is the code for my new blank page which may help...
<?php
//WA eCart Include
require_once("WA_eCart/CRCart_PHP.php");
?>
<?php
$CRCart->GetContent();
?>
<?php
// WA eCart AddToCart
if (isset($_POST["CRCart_1_ATC"]) || isset($_POST["CRCart_1_ATC_x"])) {
$ATC_itemID = $_POST["CRCart_1_ID_Add"];
$ATC_AddIfIn = 0;
$ATC_RedirectAfter = "";
$ATC_RedirectIfIn = "";
$ATC_itemName = "gdsa";// column binding
$ATC_itemDescription = "fda";// column binding
$ATC_itemWeight = floatval("0");// column binding
$ATC_itemQuantity = "".$_POST["CRCart_1_Quantity_Add"] ."";// column binding
$ATC_itemPrice = floatval("2.00");// column binding
$ATC_itemThumb = "";// column binding
$ATC_itemQuantity = floatval($ATC_itemQuantity);
if (is_numeric($ATC_itemQuantity) && $ATC_itemQuantity != 0) {
$CRCart->AddToCart($ATC_AddIfIn, $ATC_RedirectIfIn, $ATC_itemID, $ATC_itemName, $ATC_itemDescription, $ATC_itemWeight, $ATC_itemQuantity, $ATC_itemPrice, $ATC_itemThumb);
if ($ATC_RedirectAfter != "" && $CRCart->redirStr == "") {
$CRCart->redirStr = $ATC_RedirectAfter;
}
if (isset($_SERVER['QUERY_STRING']) && $_SERVER['QUERY_STRING'] != "") {
$_SESSION['WAEC_ContinueRedirect'] = $_SERVER['PHP_SELF']."?".$_SERVER['QUERY_STRING'];
}
else {
$_SESSION['WAEC_ContinueRedirect'] = $_SERVER['PHP_SELF'];
}
}
}
?>
<?php
// WA eCart Redirect
if ($CRCart->redirStr != "") {
header("Location: ".$CRCart->redirStr);
}
?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
<title>CSS PopUp Demo</title>
<script type="text/javascript" src="csspopup.js"></script>
<style type="text/css">
<!--
#blanket {
background-color:#111;
opacity: 0.65;
position:absolute;
z-index: 9001; /*ooveeerrrr nine thoussaaaannnd*/
top:0px;
left:0px;
width:100%;
}
#popUpDiv {
position:absolute;
background-color:#eeeeee;
width:300px;
height:300px;
z-index: 9002; /*ooveeerrrr nine thoussaaaannnd*/
}
-->
</style>
<!--[if gte IE 5]> <style type="text/css"> #blanket {filter:alpha(opacity=65);}</style><![endif]-->
</head>
<body>
<div id="blanket" style="display:none;"></div>
<div id="popUpDiv" style="display:none;">
<a href="#" onclick="popup('popUpDiv')">Click Me To Close</a>
</div>
<form name="CRCart_1_ATC_0" method="POST" action="<?php echo $_SERVER["PHP_SELF"]; ?><?php echo (isset($_SERVER["QUERY_STRING"]) && $_SERVER["QUERY_STRING"] != "")?"?".$_SERVER["QUERY_STRING"]:""; ?>">
<input type="hidden" name="CRCart_1_ID_Add" value="0" >
<input type="text" name="CRCart_1_Quantity_Add" value="1" size="4" >
<input type="submit" value="Add to Cart" onclick="popup('popUpDiv')" name="CRCart_1_ATC">
</form>
</p>
</body>
</html>
