Thank you @musa that code certainly pointed me in the right direction, however inserting that code exactly as you showed then overwrites the custom pdf_invoice_footer, so i changed the code slightly and concatenated it into the existing footer call.
For anyone else who wants this please see the code below and alter to your requirements:
// Set the footer if voucher is invoice and if set in settings
if (!empty($CI->mdl_settings->settings['pdf_invoice_footer'])) {
$mpdf->setAutoBottomMargin = 'stretch';
$mpdf->nbpgPrefix = ' of ';
$mpdf->SetHTMLFooter('<div id="footer">' . $CI->mdl_settings->settings['pdf_invoice_footer'] . '</div>' . '<p align=right>Page {PAGENO}{nbpg}</p>');
}
within application/helpers/mpdf_helper.php
@Developers @Contributors If you think other people will find this useful do we think it could be included as standard or at least a setting to enable/disable this function? 