After successfully charging a credit card for an invoice you get an error message:

'There is an invalid reference to QuickBooks PaymentMethod "..." in the ReceivePayment ...'

First some technical explanation what happens here:

When you successfully charge an invoice, QMerchant creates a receive payment transaction for QuickBooks. In this process we determine the payment type based on the credit card number. I.e.  the cc number is 370... , which gives us American Express. We use the first three char, means 'Ame'. Then we loop thru the payment types in the QMerchant settings (the list at the right) and use the first one we find that start with 'Ame'. If this payment method is not any longer defined in QuickBooks as payment method (somebody must have changed the payment method list in QuickBooks), the error comes up.

How to cure this now?

When connected to QuickBooks, in QMerchant, open the settings dialog. This will automatically update the payment methods. So, everything you have changed in QuickBooks is now included. Look if you have the correct payment methods selected and save.