Not familiar with that mobo, but need to make sure the Evo is hooked to the CPU Fan header. Then, in the BIOS, you should have access to some fan profiles. Possible that the default is to run at high RPMs so what you're hearing is that, not the case fans. Try cranking it down. I keep mine as quiet as possible, only spinning up a little under load.
Or, if you went from a cheap case with loud fans/bad acoustics to a nicer, quieter case, your GPU fan might be loud at idle and you just couldn't hear it on the old setup.
Thanks for the advice, turns out you are correct, it is not the case and the case fan contoller does work. I set the 212 to silent and doesn't seem to have been it. I belive it is either the PSU or the video card, both of which I was going to replace regardless.