This isn't the experience we want you to have, RobHere and Nick96.

I see the value of downloading and documenting the merchant deposit process in QuickBooks Payments. As I've checked, all of the investigations posted on this thread are closed and resolved. 

I suggest contacting our QuickBooks Payments Support again. They'll be able to pull up your account and submit a new ticket for investigation. You can use this link to reach them: QuickBooks Payments Support.

In the meantime, you can consider manually recording the QuickBooks Payment deposit. Please enter the information based on your bank statement.

Here's how:

1. Go to the Banking menu, then select Record Merchant Service Deposits.
2. Click the Add payments to record tab.
3. Hit the small arrow icon ▼ next to the first deposit on the list.
4. Review the payments in QuickBooks.
5. Choose Add payments in the Action column to add payments to the bank deposit.
6. Compare the deposit total in QuickBooks with the deposit for that day on your bank statement.
7. When everything matches, select Save and close. This groups the payments into a bank deposit and records them on your chart of accounts.
8. Review each bank deposit on the list.
9. When you've added all the payments in QuickBooks to a bank deposit, hit Record deposit.

For more details, you can read this article: Automatically record QuickBooks Payments bank deposits in QuickBooks Desktop.

I'm also adding this resource if you want to manually record invoice payments for future reference: Record an invoice payment.

If you need anything else, please let us know. The Community and I will always be here to help.