PHP Include - Need Help

[MajorFm.com]

I created a plugin as it says in the manual with the following:

ob_start();
   include('/home/sites/mydomainname.com/public_html/in.php');
   $includedphpin = ob_get_contents();
ob_end_clean();

as i want to include the in.php file in my templates

I have added $includedphpin in my header template to include it... all seems to work find but all thread links come up invalid, when i disable the plugin, it all works fine again... please advise as i really need to include this file and still have my site working fine...