For anyone else who has this problem, I was right... a simple <br clear="all" /> after last </div> solves it... 
Code:
<?php
/**
* Module Template - categories_tabs
*
* Template stub used to display categories-tabs output
*
* @package templateSystem
* @copyright Copyright 2003-2005 Zen Cart Development Team
* @copyright Portions Copyright 2003 osCommerce
* @license http://www.zen-cart.com/license/2_0.txt GNU Public License V2.0
* @version $Id: tpl_modules_categories_tabs.php 3395 2006-04-08 21:13:00Z ajeh $
*/
include(DIR_WS_MODULES . zen_get_module_directory(FILENAME_CATEGORIES_TABS));
?>
<?php if (CATEGORIES_TABS_STATUS == '1' && sizeof($links_list) >= 1) { ?>
<div id="navCatTabsWrapper">
<div id="navCatTabs">
<ul>
<?php for ($i=0, $n=sizeof($links_list); $i<$n; $i++) { ?>
<li><?php echo $links_list[$i];?></li>
<?php } ?>
</ul>
</div>
</div>
<br clear="all" />
<?php } ?>