The only difference is that one is a KUP (coach fare with instant upgrade to J/F) and the other is a true I fare (discount business class fare). Both will show up as I inventory for the int'l segments and in this case A for the domestic segments (though on a KUP it's usually P). You should earn mileage and bonuses in accordance with purchasing a first class ticket on the domestic segment and a business class ticket on the international segment.
I think the reason you are seeing that difference is the fact that one is coach automatically upgraded to the next COS (so it would see the segments in J and F as being "different") while the other is a true business class fare, so the system thinks the entire thing is in business class.
The only other potential difference is that in the case of irregular ops, AA could argue that they aren't obligated to find you a seat in F/J because you technically have a coach ticket should you choose the instant upgrade fare. I doubt this would be an issue, but technically you have a coach ticket.
As an aside, there is little consistency with these fares, as sometimes the instant upgrade will price out as more expensive because it is combining non-combinable fares resulting in a price equivalent to two one-way tickets (and to add insult to injury, sometimes the more expensive of the two will be nonrefundable). Other times, I've seen the instant upgrade fares are actually DUP fares, booking into F. It's just a mixed bag, so you are wise to really dissect what you are getting.