Had a similar issue at probably the worst station AF has (SDQ). Allowance was 2 bags + Elite extra bag, however, their system was showing only 2. Spent half an hour arguing (I could have paid the extra but I was also paying overweight on 3 bags), plus another half an hour with a "manager" who ended up verifying that I was allowed indeed 3 bags, but the system wouldn't print a third tag. I tried to contact AF when arrived to Paris, but was never able to recover the payment.