Afterburner shouldn't have any control over your case fans.
It can however, control your GPU fans. Those two cards move air and, depending on how they do it, could change the pressure properties of your case air flow.
Thanks so much, that's pretty much it then. No way it can control anything but the GPU fans. Maybe I'm just imagining this, I'll check again in a couple days and see if dust starts to build up. It's hard to tell the rotation by putting your hand over them. With all my case fans, when you try feel the air flow with your hand, the outtake and intake both feel the same, I can't feel any difference. You can't definitively feel if the air is blowing against your hand or not.