Well, it depends. Sometimes it will work like a charm and check you in all the way through, and sometimes not. It has to do with the way it was ticketed.... but I am not quite sure what the criteria is.

If you check in using the kiosk and it doesn't work, you may try asking the agent to un-check you in and have them try checking you in. They can't force a BP on AA, but sometimes I've found that when they check me in for the AS flight it automatically pops out the AA BP as well.