To get that banner to "disappear", you'll need to make the edit I suggested in post #146. As for the missing </div>, you should update that tpl_footer.php file, adding the highlighted line:
Code:
<div id="navSuppWrapper">
<?php
if (!isset($flag_disable_footer) || !$flag_disable_footer) {
?>
<div id="navSupp">
<?php if (EZPAGES_STATUS_FOOTER == '1' or (EZPAGES_STATUS_FOOTER == '2' and (strstr(EXCLUDE_ADMIN_IP_FOR_MAINTENANCE, $_SERVER['REMOTE_ADDR'])))) { ?>
<ul>
<li><?php echo '<a href="' . HTTP_SERVER . DIR_WS_CATALOG . '">'; ?><?php echo HEADER_TITLE_CATALOG; ?></a></li>
<li><?php require($template->get_template_dir('tpl_ezpages_bar_footer.php',DIR_WS_TEMPLATE, $current_page_base,'templates'). '/tpl_ezpages_bar_footer.php'); ?></li>
</ul>
<?php } ?>
</div>
</div>
The checkout_one_confirmation page (the one with the spinning icon) is displayed while the order is "processed", i.e. updating the database and sending any confirmation emails.