It is still a problem. I was unable to use RAC when I flew home on April 12 because one leg was airtran and one southwest. It was extremely frustrating!!
I'm pretty sure we booked all ours one way and we still had the issue. In fact, DM and I flew down 4 days early on AT via SW and then DH and kids flew SW all the way. We all flew home together on SW. However, we still couldn't use RAC because of that one flight DM and I took. I have stopped booking any flights that involve AT for now...too much hassle.
I'm pretty sure we booked all ours one way and we still had the issue. In fact, DM and I flew down 4 days early on AT via SW and then DH and kids flew SW all the way. We all flew home together on SW. However, we still couldn't use RAC because of that one flight DM and I took. I have stopped booking any flights that involve AT for now...too much hassle.