[Brad]

Make sure your head_newpm template is correct on all styles, it should read:

<script language="JavaScript">
<!--
function confirm_newpm() {
	input_box=confirm("You have a new private message. Click OK to view it, or cancel to hide this prompt.");
	if (input_box==true) { // Output when OK is clicked
		second_box=confirm("Open in new window?\n\n(Press cancel to open your $inboxname in the current window.)");
		if (second_box==true) {
			window.open('$bburl/private.php?s=$session[sessionhash]','pmnew','width=600,height=500,menubar=yes,scrollbars=yes,toolbar=yes,location=yes,directories=yes,resizable=yes,top=50,left=50'); 
		} else {
			window.location="$bburl/private.php?s=$session[sessionhash]";
		}
	} else {
	// Output when Cancel is clicked
	}
}
// -->
</script>

This line of code in the block above might have been changed:

window.location="$bburl/private.php?s=$session[sessionhash]";

Looks like $bburl was left out of your template for some reason.