Please make sure that you are Applying the payment. There are two steps to payments. The first part is the Manage Payments, where you enter in the payment. The second part is Apply Payment, where you apply the amount to the actual invoice. If you are in the Apply Payments screen and there are items there, then they have not been applied. After they have been applied, you can go to the Export Invoice, select the invoice and then either Preview it or Email it to see the invoice with the payment added to it.