I had the same issue. I tried calling several times, but their system basic fare does not match the price of the basic fare on Etihad.com and they are refusing to honour the price or even to look into it. One agent even said that because I searched for that very specific itinerary online may have increased the price on their system by $1000 for the same itinerary. I ended up booking through an online aggregator who match the price up to a couple of $ difference. One agent did mention that the team is working on it to allow booking of multi-city itineraries with a fare choice, so I hope it will come fairly soon.