You don't see the invoice the customer is paying
If a sales transaction doesn't appear in the list, it may still be a quote or it may have been fully paid already. To see if it's been fully paid, mark the Include Closed Sales option. All fully paid (closed) sales will appear in the list.
To see whether the transaction is still a quote, open the Sales Register window and click the Quotes tab. If it appears there, highlight it and click the Change to Invoice button. Then it will appear in the Receive Payments window and can be paid.