It was indeed the flight that caused a knock on effect. Three flights later I was on board and it didn't arrive in time for my connection. This created a 12 hour delay to arrival.
I think that the airline took an operational decision not to substitute planes to remove the delay and thus should not be able to use exceptional reasons on a flight several rotations earlier.
If Iberia has told you that the delay is because of exceptional circumstances and thus not eligible but you believe otherwise, I think your next step is to submit a complaint to AESA:
http://www.seguridadaerea.gob.es/. They will ask IB for an official report on the actual cause of the delay. You should have a negative response from Iberia in writing that you can attach to the AESA complaint.