Same here. Booked with United one way, and British Airways the other. Sorta frustrating because the return flight has some flights on AA and some on BA. So ultimately we had to go into United, BA, and AA websites but we were free to confirm seats on all legs. I believe we had the option to upgrade to business on some of the websites. For all intents and purposes it looks just like you booked the flight on Kayak.com or any other TA.
The only thing BA showed as restricted was "Changing the Flight" - which we hoped we could pull off since some folks in our party don't live in the same city. was hoping to do a "no change fee" jiggery. However it was blocked per the website at the request of our Travel agent. Which I guess makes sense.