Thank you for your post.
We do not have any performance statistics comparing Windows Server 2003 and Server 2008. On this forum, I have not heard of any performance increases from those who have moved from Windows Server 2003 to Server 2008. I have only used Windows Server 2003, so I am unable to provide you a subjective view. I'm hoping others chime in with their experience.
Have you compared the speed between your PHP interface and FileMaker's PHP interface?