WOW, this is painful. I have two flights. Codeshare on UAL from NRT - BKK and then back on an ANA flight, both booked through our corporate travel agent. Our agent was able to pick a seat on the ANA flight (very limited options) but not the code share flight. I called ANA and 3 different agents have told me that they can't select a seat or even tell me what seat I am in for the code share and that they can't change the seat on the ANA flight.

Very strange.