I have no problem posting publicly, so here's what I was able to find out - I apparently called the main number - 1-800-AIR-TRAN or 1-800-247-8726
Beyond that, I'm not sure which prompt I selected but I do recall that I was transferred and I think I spoke to a supervisor who had to facilitate the refund request. I was put on hold while that was taking place. I don't recall being transferred to Southwest at all but that was back in March. Considering that there may be less and less AirTran staff, that may have changed.
One thing I clearly remember though is that when I got the refund check in the mail, it was issued by Southwest and not AirTran.
So, this is all I remember and I hope it's useful to you in getting your certificate issue resolved. My recommendation is if whoever you end up talking to doesn't seem to be willing to resolve it for you to ask to be escalated to a supervisor.
And keep in mind one thing - Southwest has been known to reneg on their promises. Some time ago, apparently they had drink coupons that never expired and at some point, Southwest said they are expiring them and people had a year, I believe, to use them. After that, WN refused to honor them. So, I would try to get this taken care of sooner rather than later.
I was told few months ago by a Southwest agent that all RR 1.0 credits in ones' RR account will be expired after November 2nd. I found that odd because AirTran's credits are converted to points and transferred to RR but apparently, the remaining credits already in RR are expiring regardless of the expiration date of the credit. So, Southwest doesn't always bother with dates - they do what works for them.