I had a very similar problem in February of this year -- FL flight booked via southwest, maintenance issue, plane diverted back to BOS (landing gear wouldn't go up), had to wait ~5-6 hours, all passengers promised free RT. Had the little Airtran voucher too (which means almost nothing by the way, it's just a piece of paper!).

When I called to book, FL customer service said no voucher listed, but, to check with the airport FL ticket counter, since they can apparently see more information than the phone reps as it was a FL flight booked on Southwest.

Next time I was in the airport, they were indeed able to see the voucher attached to the FL PNR for the the WN flight, both of which I copied down. Unfortunately I didn't book that day, and called FL customer service later, and again same issue -- this time though, I just insisted that yes, the airport folk verified this fact, and to even double check the delay of the flight. They ended up giving me 16 A+ credits, but what an absolute pain, and they were extremely reluctant nonetheless.

My advice if you're ambitious, or if it's easy enough, would be to try the FL ticket counter the next time you're there, and book on the spot if you can. That is supposing it hasn't fully switched over to Southwest where you're at, and nothing else has changed. Best of luck though!