After running a transaction, you may find that the funds are not deposited in to your merchant account. This can be either an issue when running the card, or an issue with the payment gateway.
Review our documentation on processing a credit card sale, which includes information about how to determine if a transaction was processed. For this specific transaction (i.e. one that was run in the past), the customer's card will need to be re-run if the required information is missing.
If a transaction shows that it was processed in QuickBooks, and the correct data is present (e.g. authorization numbers, card type, etc.), there may be an issue with your payment gateway - please contact your merchant services provider.