I feel your pain. Unfortunately, the humans behind the phone lines and those operating the computer terminals are completely at the mercy of the IT/IS systems, they have little over-ride power or leeway to remediate issues like yours for precisely one reason: that is the calculated and deliberate way the airline management want it. You must play the game within their defined rules, or else you pay. They don't want the human agents thinking for themselves and fixing things, at a large airline like EK it can cause chaos and lack of oversight and control. Additionally, human agents who can not really think and have just basic common sense are generally cheaper, it's easier to get them to just follow rules and parrot whatever the computer screen says. An employee who can think for him/herself will be problematic as he/she will make decisions that may not be congruent with airline management's objectives, and will also likely be better educated and expect commensurate compensation. Basically, pay peanuts and you will get monkeys.
I am based in the US and I can tell you that your experience with the EK agent at the office is not too much unlike the experience that one can expect here, or possibly even worse.