This problem has been haunting me ever since I got my mobo back from an RMA. So basically I shut down my PC and it turns off completely, but the fans and everything else keep on running.
Mobo - Gigabyte P55A UD3
HDD - WD black 1TB
GPU - XFX 5850 1GB
CPU - i5 750 @ stock settings
RAM - 6GB Kingston KVR1333D3K3
CASE - CoolerMaster HAF 922
Hey I have the exact same problem with my PC. My original power supply burnt out, and so I had someone install a new one for me, now my PC shuts down completely, but everything stays running just like yours. From what I can gather since my problem wasn't motherboard related, is that it may be its the PSU and how it was wired. However, I'm no expert and that's just a guess.
My solution, I plugged my power cord into a surge strip and once my PC shuts down I just hit the power switch on the surge strip and that kills the power completely.
I have the exact same problem, most of my components were the same before this problem, then I upgraded mobo, cpu, and memory. Now I've got:
-Gigabyte X58A-UD3R (rev 1.0) motherboard
-Intel i7 930 (2.8Ghz) CPU
-Corsair XMS3 DHX DDR3 memory running at 1333Mhz
My PSU is quite old Jeantech 600W, not a great PSU but I did buy an Antec True Power 650W and the same problem happened with the new PSU so I returned it.
I've updated the bios to F6 (latest non beta) via the Gigabyte @BIOS flashing utility. I really can't think what else to try, only thing left is to replace the motherboard.
Don't know if you've had the same problem but my CMOS resets along with my system time everytime I power off my computer. I assumed the system battery was dead so I replaced it but the problem persists. I think the new system was working fine at first but then I seem to remember going away for a couple of days and the problem then started when I got back.
I've been builing systems for years and have come across so many problems from a faulty graphics card to bad memory but this one is truly puzzling me. Any suggestions would be much appreciated.
p.s. I've tried the basics like the windows power options and changing round the BIOS power management settings and so on so am quite sure thats not the problem.