Accounts Receivable Payment Application Error

I am having issues with applying customer payments to invoices. When I either type in the customer invoice number I get the below error. 

Error: Unhandled exception has occurred, your changes have been rolled back: Error: An error occurred during processing of the field Reference Nbr.: Error: 'Reference Nbr.' cannot be found in the system.

I have attempted to use the magnifying glass to search as well, but nothing comes up. The document is open, for the same customer that the payment is being entered for, & I don’t show any other issues that would prevent the application. We have had issues since we upgraded with the “Auto-apply” function, & have been unable to find a fix. We use a work around for applying the payments.