Thanks for your responses and advise. I have again called the TA and asked them to look into this, despite assurances that all is fine.
To answer irishguy28, "How did this "issue" come to light?" - I tried checking the booking on the iberia website to simply be sure that everything is ok, fill in any pre-departure information and also find out when check in opens. Just generally checking all was ok. From attempting this, the issue came up.
From your responses the problem could quite possibly be that the two PNRs I have aren't for Iberia, hence them not finding the details. Having said that, I did give them the ticket number I have and again they couldn't find the details. Is there a separate ticket number for each flight?