A payment might be missing from the list of payments to deposit because:
You have forgotten to select the payment in the Payments to Deposit window.
To do this task
Click Payments on the Make Deposits window toolbar.
In the Payments to Deposit window, look for the payment in the list.
If the payment is in the list, select it, and then click OK to return to the Make Deposits window.
You have chosen to deposit the payment to an account other than Undeposited
Funds when entering the payment.
If this is the case, the payment was deposited directly into the account you
specified. See if the payment went directly into an account.
Go to the Reports menu, choose Banking, and then click Deposit Detail.
Enter the date of the payment in the Date field.