I think the problem happens when you are doing an AA segment followed by a BA segment and you OLCI for the BA segment. I also think the issue is how good or "dont care not my problem attitude" the AA check-in agent in (and guess where I would categorise the many of AA check-in agents.

I had the problem flying PSP-DFW-LHR. I OCLI'd on ba.com for LAX-LHR which was the cause of the problem.

When you OCLI on BA.com, the AA agent cannot check you in for the whole route. They can only check you in for the AA segment. Thankfully as my check-in agent was struggling and there was an experience supervisor around, the supervisor reminded the agent to key the luggage tag tickets into the BA segment even though they could not check in me. It was a struggle with some manual over-rides and many agents will not know how to do this. I think the system set-up works only when the AA checks you in for both flights, even on different PNR, the luggage tag tickets are automatically copied into the BA booking.

Also, when the ticket agent starts with manual over-ride, there is a very high chance that your BP will show the dreaded SSSS for that extra security check. We had no problem with the luggage by had the extra security check (PSP is a small airport so this was quick)

In short, if you are connecting from AA to BA do not OCLI on for the BA leg. You cannot OCLI for the AA anyway and then you are at the mercy of an intelligent AA check-in agent.