Not sure I understand the AA/IB bit - are you saying this issue only occurs for AA-issued tickets (which ours are)? [Some SABRE vs Amadeus issue?]
Yes, AA-issued tickets always give some sort of trouble (although, in my experience, things have worked at online check in time). If you have a mixed IB-AA itinerary it is normally better to book the tickets through IB, as then seat selection on the AA segments still works (you can find the AA record locator through classic.checkmytrip.com, for instance).