If it helps anyone else I solved this in my project by rewriting the link when added
(function () {
var configId = '1';
var controlId = 'c1';
$('#stlivechat' + configId).bind("DOMNodeInserted", function (event) {
var chatLink = $(event.target);
var onLinkImg = $('#img' + controlId + 'on', chatLink);
if (onLinkImg) {
chatLink.click(function () {
var newWindow = window.open(chatLink.attr('href'), 'LiveChat1', 'toolbar=0,scrollbars=1,location=0,statusbar=0,menubar=0,resizable=1,width=560,height=520');
if (newWindow) {
newWindow.focus(); newWindow.opener = window;
}
return false;
});
}
});
})();