I had the same problem with BA in October: Friday's flight (LHR-MAD) boarding pass printed with BA Exec Club #; Monday's return printed with AA AAdvantage #...but both flights posted within a day or two to Exec. Club. (BTW, I had made the reservation with BA directly, and they input both #'s at that time. And separate tickets weren't an option, since my fare basis required round trip. I did use that technique with IB, though, much to the ticket agent's confusion.)

Anyway, BA said to just fax them the boarding pass and a note and they'd correct it. Waited 2 weeks and still there, so I called. "Oh, yes, I see we got your fax...we'll correct it." Wait two more weeks (it's now mid-November) and repeat. Finally got subtracted late November, but has yet to show up on American.

And I sent AA a letter in October requesting the credit (and explaining the problem); have re-sent it last week. Beginning to wonder if I'll ever get the 50K for that 5th airline!