The fares are higher if you call EK directly and the agents often can't tell which fares are saver and which are flex--especially if one way books as saver and the other flex. I have gone through this several times where the ticket was issued and the fare basis was actually a saver as the agents were clueless. If I were to book with EK, I look up the fare basis code and rules myself and have a travel agent book it for me to know for sure that I get what I am expecting.