I have had this same experience as well. My corporate travel agency profile includes a BA EC number, though I always request the TA to use my AA number instead, sometimes call BA in advacne of my flight, and always present my AAdvantage card at check-in and confirm that my AAdvantage number is printed on the BA. 90% of the time the flight does not credit properly to AA--it either credits to BA, or not at all. Each time I write a letter to AA enclosing appropriate documentation (and if it credited to BA, also to BA), and I generally have had success in getting the situation rectified, though on occasion it has taken 2-3 letters for a single flight. I always write real letters--BA will not accept e-mails for this, and in any event I prefer to have the formal documentation.