The problem all regulators face is well known, it's called "regulatory capture" - where the regulators and regulated get too palsy walsy. This can occur as a result of shared backgrounds (eg: ex air force/airline), perceived job opportunities, or straight out graft. It's not just an airline thing either.
From what I've read, Southwest had an "in" with senior FAA managers for some reason, and said managers refused to support their junior inspectors in getting Southwest to comply.
Of course, having had it's knuckles rapped for this behaviour, the FAA is now complying visibly with the letter of the law, and the junior staff whose concerns have been ignored, perhaps for years, now have to be listened too - and the juniors are bent on making right all those things that they have been successfully pressured to ignore for so long.
That's my take on it anyway, but look on the bright side, it didn't take a smoking hole in the ground to make it happen.