CPU & Case fans running after Windows shut down

I built my new pc out of all brand new parts

Here is the build:
GPU: 2GB MSI GTX 660 Ti Power Edition
CPU: Intel Core i5 3570k + Coolmaster hyper 212 Evo CPU cooler
PSU: 650W Corsair Enthusiast TX V2
RAM: 8GB (2 x 4GB) Corsair DDR3 Vengeance
SSD: 120GB Samsung 830
HDD: 1TB Seagate 7200 RPM
CASE: NZXT Phantom 410 Mid Tower
DVDRW: Sony AD-5280S-0B 24x

The CPU runs at 41-43, a restart turns the fans off briefly but when I shut down the fans stay on, even for 30+ minutes, I've tried updating the bios, but apparently I have the latest version, I've tried booting into safe mode and shutting down but windows crashes during safe mode shut down.

Any ideas?
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More about case fans running windows shut down
  1. Try the below steps to check which program is causing this problem.

    1. Click Start.

    2. Click Control Panel.

    3. Click Performance, Information and Tools.

    4. On the left pane click Advanced Tools.

    On the upper part of the window, just before “View advanced information about your computer’s performance” there is a small section which, in case something is wrong with windows 7, should report the following message: “Programs are causing Windows to shut down slowly”

    5. Click on it and find out which program is slowing down your PC.
  2. Hey, thanks for the answer, but it says "No issues reported"

    Also when I boot via VGA from my motherboard instead of booting from the 660ti, upon shut down, windows freezes on that circle thingy, so I'm thinking maybe a motherboard issue?
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