Hi david-moorlandsl, thanks for joining this thread! Matching transactions wouldn't cause any duplicated payments as it's not adding a new transaction into your books, do you have more than one payment per invoice on the system (such as a payment downloaded from LawnPro and a payment downloaded from the bank)? In all cases, our first recommendation would be to use the reconciliation tool as this will help to identify any duplicate or missing payments so that the in QB balance and bank balance match. :)
