I guess you mean IST-ATH-JMK, as IST-JMK is only served by Atlas during the summer months. At any rate, like
NWIFlyer, I'd suggest you call again, and if they say no again, ask to speak to a supervisor.
I get the feeling that A3 has hired new people who are not yet up to the level of the "veteran" CS agents (see the thread on upgrade coupons).