PHP CMS not working after change of directory

I built(using a tutorial) my CMS in a sub directory on my server and it worked fine. Admin, Archive, full display and synopsis.

I then moved all of this into my main directory, changed the index.php filename to another and used 'include' to display it within a DIV of another page.

It displays the main index.php element of the page but doesn't return articles when they are clicked.

I have searched through the files to change any instances of 'index.php' in the code but there are none. All admin functions working perfectly and the output URL onclick of blog entry is the same as the previous files in the previous directory. Of course without formatting but that is no problem.

In what part did I make a mistake? I would like to avoid using an iframe to resolve this issue.

The code that the index.php file is including. (homepage.php)

<?php include "templates/include/header.php" ?>

  <ul id="headlines">

<?php foreach ( $results['articles'] as $article ) { ?>

    <li>
      <h2>
        <span class="pubDate"><?php echo date('j F', $article->publicationDate)?></span><a href=".?action=viewArticle&amp;articleId=<?php echo $article->id?>"><?php echo htmlspecialchars( $article->title )?></a>
      </h2>
        <p class="summary">
        <?php if ( $imagePath = $article->getImagePath( IMG_TYPE_THUMB ) ) { ?>
          <a href=".?action=viewArticle&amp;articleId=<?php echo $article->id?>"><img class="articleImageThumb" src="<?php echo $imagePath?>" alt="Article Thumbnail" /></a>
        <?php } ?>
      <?php echo htmlspecialchars( $article->summary )?>
      </p>       
       </li>

<?php } ?>

  </ul>

  <p><a href="./?action=archive">Archivo de Articulos</a></p>

<?php include "templates/include/footer.php" ?>