I just jumpseated on Airtran on Monday, when I got to the gate the agent would not list me for the flight, and sent me to the service counter to list.
It was about 45 mins from departure so it was not a problem, however if you are running late you will miss the flight.
I have been told something different every time I have jumpseated on Airtran. If I go straight to the service desk they send me to the gate.
The Airtran crews are among some of the best, and will do everything they can to make you feel at home. The gate agents are either very good or just not very helpful. Thanks for the rides though to all the Airtran crews. (pilots and FA's)