One thing that I know can work when one of the legs is international (and may work here) is to keep calling until you get an agent that will split the flight. This way it will show as separate segments and you can upgrade one. If it work, it will have the added benefit of getting the segment mileage. Given that they may well change planes anyway, having the same seat is just a computer artifact.

As I said, I've done it for a domestic/international "direct" flight. It's worth a try.

Cheers.