Do you still have the e-ticket receipt? I would say just do it the old fashioned way and mail in your BP stub and e-ticket receipt that shows the booking class. If they still deny it, you might be out of luck, but give it a shot that it's just a problem with their electronic system.

I was recently denied credit as well through the automated system, for a TG flight in D on a ticket that was issued by UA. I mailed the BP and ticket receipt in--we'll see what happens.