Your situation is not unique. Though I would have thought that if you were in the check-in queue 15 minutes before the cut off, they should have serviced you or called out before the flight was closing. And they normally do that considering that that was the only EK flight departing at that hour there wasn't much any other reason why you would be standing int he queue. And why would you let another person get ahead of you (or the person wanting to get ahead of you) when you both know that you are checking in for the same flight?
Take a look at this thread.
http://www.flyertalk.com/forum/emira...mins-late.html