Works fine here.
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 3.2//EN">
<html>
<head>
<meta name="generator" content=
"HTML Tidy for Windows (vers 25 March 2009), see www.w3.org">
<script type="text/javascript">
var newWindow ;
function FNUMBER(SOP)
{
newWindow = window.open(SOP,'','left=0px,top=0px,width=800,height=670');
setTimeout('newWindow.close();',5000);
}
</script>
<title></title>
</head>
<body>
<form>
<input onclick="FNUMBER('http://www.google.com')" type="button" value='test'>
</form>
</body>
</html>
Google opens, and 5 seconds later it closes.