The relative links would be set one way in your Zen Cart header and another way in your root header ...

You are at different levels of the directory tree and what works in one does not work in another ...

You have to look at each header separately ...

The Zen Cart shop header could probably use:
Code:
<a href="/Articles/index.html">ARTICLES</a>
That takes you to the root, then looks for the directory /Articles and then runs the index.html in it ...