I’ve had the same problem checking in luggage at the EI check in. I joined the queue with 45 mins to go before check in closed, knowing full well that it would take longer than that to get to the front of the queue and would ultimately result in me having to go to the ‘closing flights’ desk. I asked if I could just go to the closing flights desk and save myself the time wasted queuing, but no – please wait in line until your flight is closing. The situation was absolutely crazy with the terminal chockers full of people. It was a Sunday too.
Instead of being able to grab a bite to eat before the flight (and spending money in the airport) I spent the time wasted standing in line to drop off a bag. EI really need to address their check in at busy times, waiting for an hour to drop off a bag is totally unacceptable.