$_SERVER['DOCUMENT_URI']. will echo the directory you are in so it will always cause a problem. is this not ok or is it interfering with your .htaccess somehow?
<ul> <li><a href="<?php echo 'index.php'; ?>">Organisation</a></li> <li><a href="<?php echo 'about/organisation.php'; ?>">Organisation</a></li> <li><a href="<?php echo 'about/team.php'; ?>">Team</a></li> </ul>