Zero balance not picked up in subsequent payment

We have instances where an old invoice and credit are on the system creating a zero balance. A new invoice has then been input to the exact same supplier details. When the later invoice is paid, all 3 records are picked up on the Selected Schedule Payments report, but the old invoice and credit note are then dropped off and only the recent payment issued.

What would be causing them not to be picked up and cleared when the supplier balance is back over zero?