This has also happened to me a number of times in the last 15 months when I fly especially to PAP in the summer where there is an embargo issue to further complicate this. I got tired of trying to convince the check in agent so I resorted to calling the EXP desk and having them put a note in my record locator. also they claim can't put more than two bags to be checked (legacy US agent)! There is a way around that just need to find someone who does know how on the AA side.

One time i had the EXP agent on the line who agreed I had a 3 bag allowance while at the counter and the agent who disagreed would not talk to them. I ended up having the EXP agent annotate my record and then got the agent (reluctantly) to look at the note. They were about to charge me $150!