All fans run when system shut down

I have an msi motherboard and know that there are various fan settings in the bios.

Have you checked the smart fan settings or tried resetting the bios??

try resetting cmos
http://www.youtube.com/watch?v=Pdp_L5IxaNI

update bios(if not thats fine)
http://www.tomshardware.com/forum/308518-30-update-bios

check psu
http://www.youtube.com/watch?v=5FWXgQSokF4

make sure atx12v
http://www.tomshardware.com/forum/261145-31-perform-ste...

Hope this helps it sounds like a psu or mobo issue to me

hey guys, thanks for the feedback. i should have mentioned, i've tried 2 different motherboards in this machine. i had an intel z68 board in there originally, it did the same thing for a while (fans full when off, worked fine / good temps when on), eventually it refused to post anymore with the "hot cpu" led lit up. this light would come on instantly as soon as power was supplied to the board even though the cpu has sat cold with no power for days. i figured the board was defective (bad heat sensor or something, and the bios code display had never worked) so i replaced it. the new board boots fine, everything works perfectly with the exception of the fan behavior, and post bios code "A0", which the manual is very vague about ("Onboard devices Initialize and Detect")

i've tried resetting cmos on both boards, latest bios, tested psu with paperclip test (and computer boots up and has power fine), mobo and cpu power are all plugged in securely.

please let me know if you have any thoughts,
thanks for your time

well with 2 different motherboards we have ruled out bios

Take panic's advice try a new PSU

one other thought, this is a stupid question, but want to make sure I am covering all the bases, there is no extra or 3rd party fan control is there? no 5.25 bays with switches or rpm displays?? or anything like that??

Which fans (CPU, chassis, PSU) fans are running and what are they plugged into?

wow, thanks for getting me to try swapping the psu, i had to pull it out of another active machine so i never would have tried unless i had more reason to believe it was the psu...
ocz pro 700w modular psu = fan problems
$20 400w thermaltake = works great  

now i just need to decide if it's worth keeping the msi z77a-gd65, or get my money back and give the intel DZ68BC another try.

hmm well i dont know i mean you already have it right... But glad it works and glad we figured out the problem!

Best answer selected by station.

thanks again panic, went back to the old board and working perfectly with the alternate power supply, saved me time and money, should have asked here earlier  
anybody want an ocz 700 watt paperweight?

XD yes!