There were some fixes for that in some of the newer releases.
Essentially, there is a line in the bottom of /includes/classes/order.php, which should read thus:
Code:
$html_msg['PAYMENT_METHOD_FOOTER'] = (is_object($GLOBALS[$_SESSION['payment']]) && $GLOBALS[$payment_class]->email_footer != '') ? nl2br($GLOBALS[$payment_class]->email_footer) : $this->info['cc_type'];
To locate that line on your installed version, simply do a search for ['PAYMENT_METHOD_FOOTER']
Then make the appropriate adjustments.