Just incase some-one reads this because they have the same problem, here is my (limited) solution. Todo normal order status updates I use the existing ZC orders functionality and only when I want to edit an order do I use edit orders, however without sending a confirmation to the customer since this is when the error occurs.
To achieve this I changed admin/orders.php to only call edit orders when I click on [Edit] (at the end of the order listing in the rigfht hand column) however when clicking [Details] on the top right hand column to call the standard details page from ZC from which the notify customer function works.
To acheive this you need to find this line (around 781):
$contents[] = array('align' => 'center', 'text' => '<a href="' . zen_href_link(FILENAME_ORDER_EDIT, zen_get_all_get_params(array('oID', 'action')) . 'oID=' . $oInfo->orders_id . '&action=edit', 'NONSSL') . '">' . zen_image_button('button_details.gif', IMAGE_DETAILS) . '</a> <a href="' . zen_href_link(FILENAME_ORDERS, zen_get_all_get_params(array('oID', 'action')) . 'oID=' . $oInfo->orders_id . '&action=delete', 'NONSSL') . '">' . zen_image_button('button_delete.gif', IMAGE_DELETE) . '</a>');
and replace
FILENAME_ORDER_EDIT with FILENAME_ORDERS
