A little more information..
The page works fine right after restarting apache.
My .htaccess index.xml and nav.xml files.
------- .htaccess ---------------
DirectoryIndex index.xml
<Files index.xml>
PerlHandler AxKit
AxAddProcessor text/xsl /xslt/menu.xsl
AxAddProcessor text/xsl /xslt/page_html.xsl
# AxAddProcessor text/xsl /xslt/dbi.xsl
</Files>
---------------- index.xml ---------------
<?xml version="1.0"?>
<page
xmlns:xi="http://www.w3.org/2001/XInclude";
>
<title>Welcome</title>
<nav>
<xi:include href="nav.xml"/>
</nav>
<body>
<h1>Welcome to the Education System</h1>
<p>If you are here, you should have an account with which you can
login.</p>
<p>If not, ask your professor about getting one</p>
</body>
</page>
-------------- nav.xml ----------------------
<?xml version="1.0"?>
<div>
<em>Navigation</em>
<a href="/advise/" >Advising</a>
<a href="/question/" >Physics</a>
<a href="/evan/" >Evan</a>
<a href="/chuck/" >Chuck</a>
</div>
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