My guess is the proper MCT is somehow not being applied. The AY service is a new one this summer starting up in mid June, so it might not have been properly setup. You can't book a AA-BA ORD connection at 38 minutes, so I wouldn't expect 39 minute AA-AY one to work. Call AA, and hope you get an understanding agent, rather than one that simply says its legal because you can book it, or the computer says its fine.
Incidentally, I am flying the other leg, HEL-ORD, a few weeks later. The connecting flight I was originally booked was removed from the schedule, now leaving me with a 1:40 connection at ORD on the last flight to DFW that evening. I guess I should be wearing my running shoes.
The only upside is the equipment is now showing up as a 788.