I am having similar problem too! Yesterday I decided to programm a payment module and I was mostly successful. Everything worked like a charm, until I looked inside the order finally and I have seen that warning. Where is the second payment coming from???? I am adding a transaction number to my orders and my order doesn't have the invoice whereas the other one, not generated by me, has one. Please point me to a point, where I could start searching. I am slowly going crazy because of this