If the Payment History shows the payment coming out, do the following:
Open the Customer record
Go to the History tab
Scroll down in the Payment History and look for the Payment coming out of the order
Confirm you see the payment going into Customer Credit (Order of 0 with the payment amount)
Go to the Financal tab and confirm the customer has the credit for atleast the amount of the payment
Go to the Payment window
Select the Apply Credit button
Apply the credit back to the order