If you pay with a credit card you are protected if the airline goes bankrupt or if there are other irregularities. If you pay using the same credit card but through PayPal then all your protection and insurances fall away. I only just recently learned about this despite having been flying for quite a few years now. Never use direct debit cards. Could the direct debit card somehow be the cause of the problem, I wonder?
I hope that the several upcoming bookings I made with airberlin using PayPal will be ok! There is a possibility that the airline could go bankrupt during the coming months.
PayPal is, however, useful for certain other purchases because there is a very good conflict resolution department. I am speaking from a European perspective though, and here it is permitted to charge large bogus fees for using a credit card to purchase airline tickets. That is the reason I was using PayPal.