hi.
I have similar problem but for me , i use mass action for on after order confirmed redirect to some joomla menu. i use this code in Run PHP code box:
$url="index.php?Itemid=337";
JFactory::getApplication()->redirect(
JRoute::_($url, false)
);
and when i disable that , the cart empty successfully.
i can set return url in payment method but if user use 100% coupon it is not work.
even i use that code in the plugin but the problem is still and cart not empty.
i write my redirect code at the end of checkout/after_end.php and it is work without problem