I sent an overdue statement to a customer. It showed the correct amount due, ($3743) however, the online payment showed that she owed $1. I resent her invoice, however the same problem occurred, showing the correct invoice amount, but payment screen showing she owed $1.
Have you tried deleting and recreating the invoice? That will let us check if the link between the actual invoice and the online payment is broken.
If you've done that already with similar results, please contact our Merchant Services Department. They can take a closer look at this to determine why the online payment is giving your customer an incorrect amount.