I liked airtran's service to/from Boston (all staff members were very nice, the captain joked around with us and the flights were good), but I hated the seats - Something about them threw my back off and I counted down the seconds for the flight to land an hour into it both times I flew with them (once was in Sept, the other in Jan - the SW flights I took on that trip gave me no such issues.) So, you're not crazy, nor are you alone.
I usually fly SW, but also have no issue with other companies. My theory as to what happened: the legroom was smaller than what I was used to and I recall on one trip, the person in front of me was jamming their seat into my knees. Also, there was some sort of small metal box on the floor in the under-seat storage area both times. My luck.
Are you and your wife tall?