SEPA wire transfers are actually not processed instantly. Banks are allowed to take up to one working day. Also, there are still numerous banks that charge a fee per transaction.
I think that's the rule rather than the exception.
This means that if your bank charges 0€ for national transfers, it cannot charge for SEPA ones (the ones with IBAN). But it could in theory charge for national and SEPA wires.
http://en.wikipedia.org/wiki/Single_Euro_Payments_Area#Misco...