Kwthom pointed out that you can't have two separate rides with the same miles, so therefore even though the SS2K would have included the JAX miles, the person certifying the ride cut it off at Tallahassee.
Is that all you paid for? You can choose cert only, or full swag and cert. If you paid for full swag and cert, you normally get that all together at the same time. It's possible someone simply made an error and if so, you should ping them about it so you get what you paid for.
I saw these certificates on a facebook post, and since I just completed my 50cc in the same month, it got my 'radar' up. So I am now thinking of re-submitting the necessary paperwork for the SS2K, or does it need to be done at the same time that I submitted the 50cc?