Maybe, it is a case of using two instances of a specific id named control in the same web page, something that is irregular for html coding....
Regarding the popup window displaying when the home page loads, you just place the popup window code without using any function and link, e.g. something like:
Code:
<script language="JavaScript">
<!--
window.open('new_product_url','windowname',' height='320,width=320,scrollbars,resizable');
// -->
</script>
You could place this code for example, inside the welcome.tpl template file, so it will execute only when your home page first loads.