Computer won't fully turn off when powering down.

Hi everyone,

So for Christmas I got a new case, power supply, and graphics card (to crossfire).

Since moving to my new case, I've noticed that there's been an issue I haven't been able to fix yet. When I turn off my PC (lets say via Windows) it does the normal shutdown process, the monitors turn off, the OS shuts down, but it seems that most of all fans remain spinning after the OS has shut down, this includes CPU heat sink, graphics cards, front case fans, etc. The way I have to turn everything off now is by flipping the on/off switch on the power supply itself. I can then re-supply the power by flipping the switch back on, and the fans will stay off until turned on via the case.

This issue is just becoming more of an annoyance rather than anything else, being that I need to turn off the computer through the back instead of the front. I'm looking for any possible fixes.

I've already tried clearing the CMOS on the motherboard by holding the CLR CMOS button on the motherboard for 5 seconds, and after it being successfully cleared the system still did the same thing. Additionally I've tried reinstalling Windows 8.1, not that this would be a fix, but I was going to do it anyways.

Anyways, does anyone have a suggestion? I'm open to anything. Again, the issue only seems to occur after I switched it out this new one with my old one. (CoolerMaster HAF 912). So after a new PSU, Case, and an additional graphics card, this issue has arisen.

Thanks.

SPECS: Operating System - Windows 8.1 x64 // Motherboard - ASRock Z77 Extreme4 // CPU - Intel Core i7 3770k @ 4.0GHz // GPU 1 - AMD R9 290x 4GB // GPU 2 - AMD R9 290x 4GB // RAM - 16GB DDR3 // Case - CoolerMaster Silencio 652s // PSU - EVGA 1000W (G1)