My experience is that BA and AA IT don't communicate very well with each other. I've had this happen to me, with an initial leg on AA connecting to BA. BA wouldn't let me checkin until the AA segment was checked in (the error message you get isn't helpful, I don't remember in detail, but probably the "Our systems are currently not responding, please try later"). AA couldn't checkin on line for some reason I never understood. I finally called them up (very easy, no holding and someone in the USA who spoke English) and they pushed the magic buttons allowing me to checkin, but still requiring me to go to a desk. And even after I had checked in subsequently on BA, I still got paged to go to an agent in LAX.