I figured out my problem. When I went to Receive Payment, I was entering an amount in the Amount Received box in the header. Then when I checked the invoices that were being paid and finally selected a credit at the bottom (the bank deposit), it was leaving the customer a negative balance in the A/R aging. Essentially, by entering an amount received in the header, I was saying that the amount had been received over and above the amount of the credit. When I blanked that out to zero, selected the invoices to be paid, and then select the credit and the bottom, everything worked out fine.
