I was flying only EK, no other airline. My problem was I was changing flights and going on a different passport. And that is why the complexity of my pnr. It happens to me often and EK have either checked them through from the starting station or done if at transit in Dubai.
It takes them a while to figure it out, but the check in agent has helped me. And I am very grateful, because I usually arrive in the middle of the nights and transfer a couple of hrs later. So obviously am dead tired.
And the old adage holds true, you attract people with kindness and gentility. Am always grateful when they go the extra mile for me, and make sure they know it. I usually gently ask, and when they show it could be a problem and back out gently. It has never given me bad results.