I had a similar experience last year. I was looking at flights and Airtran.com and Southwest.com both had a very high price. I checked Expedia and Travelocity and both showed seats available on Other Airlines at much lower prices and seats on Airtran for that same lower price. I never could get the Airtran ticket to go through and eventually made other arrangements. Next time I'll call Expedia.
Looks like Southwest's legendary IT team has taken over at Airtran.