Prepayment request and final invoice

Can anyone help with a question about posting payments to a prepayment request and then reconciling the final invoice. We create a sales order and then a prepayment request for 100% of the sales order. The customer then pays for the goods. We put in the payment under the incoming payment screen against the prepayment invoice. This then closes the prepayment request.

We then ship the goods to the customer creating a delivery note from the sales order. Then we create a final invoice for the customer. All OK so far I think. Then the help page tells me to go again to the incoming payment screen, select the business partner and then select the prepayment invoice and the final invoice and all will be OK. BUT we cannot add the incoming payment because we get a message " Confirmation amount must be > zero".

What are we doing wrong. We have tried to do a standard reconciliation in the banking module, but this leaves a double posting amount in the VAT account.