did you solve the problem?
Otherwise - the support (i.e. twitter) could give you an Amadeus PNR if you booked directly via Iberia.

I had the same problems - your flights inside the eu you can check in when you want. During the check in you can enter your FFN and choose seats. (the only way it works, oddly travelling with wife and two children - only my BAEC couldn't be entered in the mmb)