Are you saying the JAP50BMI exists between BNA and MAN but bmi itself can't book it? Even at a ticket desk? Strange.
I often have the same problem departing EDI - through-fares are loaded from MAN, but the extra sector seems to cause problems. As a result, I try and do as much ticketing as possible at the EDI TD. Helps to keep them in a job, too ^
Does JAP50BMI exist between ORD and MAN? What would be the extra cost of booking a revenue ticket from BNA to ORD?