Let's make sure that we'll be able to fix the issue with your payment, ChezC.
QuickBooks Online (QBO) integrates and works with several third-party applications. However, it is dependent on the data that is being passed on. You can disconnect and reconnect the app so it will refresh the connection. Once done, double-check if it's already correctly matching the payments.
Apart from this, QuickBooks normally takes care of invoice payments processed with QuickBooks Payments for you. You can learn more information from this article: Deposit payments into the Undeposited Funds account in QuickBooks Online. If the issue persists, I recommend contacting our Payments Support team so they can investigate this issue further. They have the necessary tools that they can use if there's a need to escalate this to a higher tier.
Also, after a thorough process of matching your transactions, you can now start with your reconciliation to ensure that the actual amount of money spent matches the amount shown leaving from an account. You can visit this article for detailed steps: Reconcile an account in QuickBooks Online.
Please touch base with us if you have any concerns or behavior that you encounter with your CRM integration. Remember, we're here to make sure that everything is well taken care of.