With eCart the order should be stored into the db on the confirm page. The id for the record that is inserted is stored in a session variable. This same session variable should be what you see in the email receipt.
$_SESSION["FQPWholesale_OrderID"]
If this session variable is not being set you will not see it in the receipt, but if it is set then it should appear in the receipt. Do you know if your session variable that is created in the Store Order Summary server behavior is name like this? If you can post back with the confirm page minus the sensitive details in a zip archive I will take a look to see what I can find for you.
