If the flight is available at the supersaaver level on aa.com then you will to call your BAEC service center to book. There have been a few reports that ba.com has a problem with displaying all of the flight options available if there are more than nine, iirc. It will just drop off the later flights. As a result if you need to book those flights you will have to call.
I can only find one of the threads at the moment. See:
http://www.flyertalk.com/forum/briti...not-avios.html

If the capability to book is available online but not currently working correctly then you should be able to have the offline booking fee waived.