PHP include problems

[test1man]

I'm having a problem with php includes and contribute. I use a php include to
bring in my header and footer with the following code.

<? include ($_SERVER['DOCUMENT_ROOT']."/includes/header.php"); ?>

Sometimes in contribute when the document will publish it will save the actual
contents of header.php in the file itself and replace the include line. This is
a huge problem b/c if I make a change to the header it no longer applies to
that page. Has anyone else had this problem before? I'm using both contribute
3.1 and 4 and I seem to only notice it in 4 at the moment. It looks like it's
writing the file out like the browser sees it rather then how the actual code
of the template is.

If no one knows why this is happening is there at least some code I can use to
tell contribute to ignore an include?

[test1man]

Can someone please help out with this? It will probably take some actually from
adobe to answer this question but it is a very serious problem. I use
contribute all the time and sell it to all my clients but if this can not get
resolved I'm going to have to look into other CMS solutions.