Currently the VQmod XML file used to edit the footer template is hard-coded to edit the default template footer file;
<file name="catalog/view/theme/default/template/common/footer.tpl">
<operation>
<search position="before" offset="1"><![CDATA[</body>]]></search>
<add><![CDATA[
<?php echo $piwik_footer_text; ?>
]]></add>
</operation>
</file>
If a custom template is used, this will not make the modifications correctly.