Could be wrong but I understood MAD / JED as a surface segment which should make it valid for a DONEx. Also makes sense since IB doesn't fly to JED and the OP didn't indicate any connection getting there.
Ah, yes. I didn't spot that. So a Valid DONEx 
Are any segments giving you economy only instead of business? That can cause pricing issues in the tool.
Yes this causes a problem in the tool. It shouldn't but it often/always? does.