Ok what I meant was that there is a large technique for developing "dynamic" php websites.
You have you main structure files that get reused over and over.
If you are set up in something like that so when you click a link you are not actually going to another webpage, but are changing part of the php on shown (which it sounds like since it is being displayed on all pages I think?!?!). then you need to change the file that the link is point to for the home page only and not be part of the background code.
But if you do not have it set up that way or can follow that then it means I have to explain it differently.
So need to know some of that info... like whats the code you are working with to point u in the right direction.