I went to your site and visited the iSearch/index.php file.
There are TWO headers being used on that page it appears because there are 2-head sections, 2-DTDs, and 2-opening Body tags <body>
Furthermore, I recommend getting rid of the the javascript that is used for the menu entirely. It uses a TON of code that is not really necessary. All of that code be done with a few lines of semantically correct markup and a little CSS.
The path to the Flash (../images/flash/intswf.swf) file used in the header is either incorrectly specified, or the file really does not exist.
if you want to include the header in the root directory from within a directory one level down, you may do this:
<?php
include('../header2.php');
?>
You don't need to use an absolute path. Just use the "../" to specify that the file exists one-level-up...