I've had the same thing happen twice... each with completely different outcomes.

First time, I showed up 40 min before departure and was told the flight was closed. Unfortunately there weren't any other flights that night, so the agent marked my bag as a 'Late Bag' and told me that if it didn;t make the flight, they woud send it on the next available flight, but it would be my responsibility to come pick it up. Bottom line is I made my flight and so did my bag.

Second time, I showed up 40 min before a TED departure and was told I had to get rebooked as I missed the cutoff. Instead of markingit as a late bag, I was told I had to sit in SFO for 10 hours (with my 4 yr old daughter) until the next flight I could be confirmed on. No amount of pleading, reasoning, or logic would sway this agent in her ways.

Its hit or miss with the agents you get... and unfortunately you can't "hang up and call back" when you're standing there in line.