Consider me a detective on the case to find those missing payments. To begin, verify the selected QuickBooks Payments deposit account in your company settings with these steps:
Verify Payments Deposit Account
From QuickBooks Online, click the Gear icon (⚙) and select Account and Settings.
Select the Payments tab.
In the Deposits section, check which account is selected under Change Bank.
This is the account that QBO will place deposits in by default. The information here is also available from our guide on updating your Payments deposit account. If the deposits still aren't appearing in this account's register, I recommend looking into Undeposited Funds to see if they're hiding there. These instructions will help you accomplish this:
Check Undeposited Funds for QuickBooks Payments
From QuickBooks Online, click the Plus icon (+) and select Bank Deposit.
Look beneath the Select the payments included in this deposit section for the words QuickBooks Payments. Click there to expand the section.
If Payments weren't automatically deposited to the account selected in the steps above, they'll appear here and can be deposited using this screen. Just check them off as needed and select Save and close once the total matches the value of the deposit on your bank statement.
The QuickBooks Online Test Drive company doesn't have a Payment account with which to demonstrate, but this brief video example shows where the payments will be located on your Bank Deposit screen:
Once the payments are deposited from here, they'll appear in the bank register you have selected in the Account box on the screen above. Please let me know if this helps you get to the bottom of those missing payments. Thanks for bringing your question to the Community, I'll keep an eye out for your response.