I ran into a similar situation with Aer Lingus last. I was looking for tickets for Hartford-Venice/Milan-Hartford and could not get them on the Aer Lingus website. The itinerary was available on Expedia. Since I prefer to book directly with the airline, I contacted Aer Lingus to ask them about this. They responded but did not explain why the itinerary was not available on the website. I ended up using a different airline and a different departure city for the trip anyway. Friends of ours were looking for a similar flight to Italy, and I reluctantly advised them to use a third party site.
We like Aer Lingus because it is the only caririer that flies directly to Europe from our home airport. Also, we like being able to go through US customs and immigration in Dublin on the way home.
1885BD has a good suggestion. I would also try the British Airways website, since BA is the parent company of Aer Lingus.