I think they are referring to the $1 (or so / can't remember the exact surcharge) per coupon ticketing fee that myIDtravel adds on top of the interline fare. Maybe EK was charging twice that amount? I doubt they'd get away with unilaterally doubling the Zone fare.
EK is however quite proficient in withholding refunds over extended periods, especially from its own staff, not just for tickets but for medical claims also. While it is paid eventually, the company surely makes money in interest from holding onto the cash for a minimum of 30 days or more. Not to mention the fact that staff may forget after protracted delays to chase it up and therefore lose the whole amount outright.