Hi there,
I recently had the opposite experience at SFO - I was the guilty one arriving late.

I was meant to fly at 13:50 SFO-ORD then connect onto my flight back to LHR. There was a wreck on the 101 freeway and I arrived only 50 minutes before departure. I was confronted by a giant queue. I waited in line and then was pulled to the front to check in.

Fortunately, the SFO agents were clever enough to avoid trouble and only 1 of the 5 agents (of the section I was in) was processing the late comers.

I know the rules and guidelines and by rights I should have been looking at a standby ticket on a later flight. It worked out for me this time but I agree that it's not a particularly fair system. Everybody is made aware of the rules - if you cut it fine you shouldn't expect to queue jump.

Jason