I think this sort of problem is not unique to Airtran. I've encountered this many times on serveral other airline sites, as well as many of the online travel sites. Seems to be more an issue of the day of the week, and time of day when you're trying to make the purchase. Usually late at night based on USA East Coast time, and middle of the week.
Just had this very issue with Continental, and Orbits last week Wednesday when trying to book a 6:30pm flight to Houston. It wouldn't show as available on Continentals site, showed as available on Orbits. However, when selecting this flight on Orbits and attempting to purchase it the flight was no longer available. Then, I look at Continental again and its available. Trying to purchase it and its gone.
Next morning for me, which is about Noon Eastern time, everything was fine. Flights were there and the purchase could be made. I see this regularly because of the significant time difference.