When I create an invoice from scratch (ie not using billable time), it always displays a PAID IN FULL stamp and shows within the list of invoices as PAID IN FULL. Clearly it isn’t ‘paid in full’ until money is received and logged against the invoice.
Total amount is credited, thus appears Paid in Full stamp.
Did you receive an overpayment for this customer. If so, amount is automatically credited.
Have a look in Summary tab under Customer credits (amount on right is a link).