In my header and footer i've got the HTML for the layout of my site.

include_once("$root/includes/header.php");

switch($mode)
  {
  case "newmap":
  include("$root/docent/newmap.php");
  break;
  }

include_once("$root/includes/footer.php");

inside the file newmap.php if got the php-code that i use for the site inside this code ive got some error-windows for the users. I use the script below to call them inside the file newmap.php

if (mysql_num_rows (mysql_query("SELECT pparent FROM pagina WHERE pparent ='$menu->id'"))>0)
   {
    ?>
    <script language="JavaScript">
    name = "<? echo $menu->name; ?>";   
    window.alert("Cannot remove'"+name+"'..!  This map has one or more submaps, remove this first....!!")	
   </script>
   <?
   }

My problem is that in this switch structure the javascript runs first and i get a window but my site disapears (loses the header and footer) and when i push "ok" in the window it jumps back to the php. including header and footer again does not work. 
 
When i do this with a if else-statement i haven't got this problem. And i see the whole site with a javascript window in front. Is this a bug?? 

Thanx anyway Greetings Ivan Spijkers