Payments made through QuickBooks Payments, whether by credit card or ACH transfer, are marked as paid immediately on the invoice. However, please note that deposits take some time to process, normally 1–2 business days for credit cards and 2–7 business days for ACH transfers.
To fix this, I suggest viewing the transaction information directly in QuickBooks and in the Merchant Service Center.
Here's how to do it:
Select the Gear icon and choose Account and settings.
Go to the Payments tab and select Manage details. This will open your Merchant account in a new tab.
Choose Transactions from the Activity & Reports menu.
Find the payment and select it to see extra details, including the name, email, or the last 4 digits of the card used.