Hi, old thead but I think many users may appreciate an answer.

The same thing happenend to me. I booked an American airlines flight. Usually, I pay using credit card. This time, I used Paypal (Paypal balance).

I received emails confirming my reservation. However, my Paypal account showed a "pending" American airline payment. The corresponding amount of USD was no longer available on my Paypal account balance.

It took 48 hours for the payment to be "completed".

I believe AA had to confirm my ticket for Paypal to release their payment.