My experience is that there are no Paypal fees.
I also find that you need to have sufficient Jetstar vouchers to cover the entire booking. So you'll need your 3x $500 plus some smaller ones to make up the difference, otherwise the booking fees come back in their entirity. Make sure the default $2 donation is deselected, because jetstar vouchers don't cover that, and they'll slap on the booking fees to cover that $2 payment.
Wierd in the world of Jetstar