Just had the same thing happen to me 5 minutes ago when I was helping my Aunt and Uncle book EZE-JFK-ORD (all AA metal) flights in C over the phone.

The itinerary that we wanted couldn't be booked on the web as BA.com couldn't pull up JFK-ORD segment although it was available. But when we check EZE-JFK AA metal on BA.com, taxes came to only $59.00. But over the phone, the agent quoted us $236.50 ($59 + $2.50 + $175 YQ). We politely objected the quoted YQ by explaining our rational of BA.com not showing YQ. The agent then put us on hold and after more than 40 minutes came back and explained that she spoke with her supervisor who explained that charging YQ on AA metal for award tickets was part of the AA-BA-IB deal and its just that BA.com system has not been updated to reflect the same. But it should happen very soon.

We then also added ORD-YYC as an add-on and were YQ'ed ($74) that segment also.

Regardless, we went ahead and paid YQ to book the tickets as we were getting ideal flights.

But what a bummer!