Hi kcport
Thanks for your post. If you've already entered a corresponding transaction in MYOB, you should match the transaction. See Matching bank transactions. A bank transaction and MYOB transaction are matched if they have the same date and amount and the MYOB transaction is the correct type (such as Spend Money). If there are two identical transactions, a match won’t happen — you're able to review the possible matches and select the right one. This is not something that can be switched off.
How was the payment linked to the invoice? If you’re receiving a payment from a customer for an invoice entered from the Invoices page, enter the payment from the Invoices page. For more information see Customer payments. This article also describes how to delete a payment.