I would check all of your fans and make sure its not one of them vibrating against their mounts. Make sure all your screws are tight. If those all pass your examination, then I would move on to the HDDs and much absolutely certain that its not one of them making the noise.
Your note about booting from one HDD or the other makes me thing almost certainly that it has to be your HDD, even though you say its not. Double check to make absolutely sure.
I know what that sound is. Its your CPU down-clocking. My AMD Phenom does the same thing, its some sort of voltage regulator buzzing on the motherboard. It usually happens when Cool and Quiet slows my CPU to 910MHz down from 3.5GHz.
Can I ask you notsonoobPCguy, do you find this noise anoying and even disturbing? Or is it just my "too aware ears" that are complaining for nothing?
Did you find a cure to this noise problem? To me, doesn't seem to be normal this kind of CPU noise, especially since it was absent while running windows XP 32bits. Is 64-bits OS that demanding? Shouldn't the noise stop while I'm working on a plain txt file for 20 minutes???
To answer you first question, yes, I got a new motherboard but it wasn't because of the CPU sound. The MSi board i just got is a lot quieter then my old ECS one but i can still hear some sort of buzzing if i either listen really carefully or have my case open. The sound matches what some Blue LEDs on the mobo do, they are some sort of Cool and Quiet option. About it not happening in 32Bit XP, maybe XP doesn't wont let the CPU down clock? Just a guess. You might want to try disabling EIST or SpeedStep in your BIOS. Its the C&Q equivalent for Intel. Also, have you taken off the metal PCI extension covers? Those could be leaking sound.
Check this out http://www.overclock.net/intel-cpus/672338-intel-core-i... Someone has the same problem. A use mentioned in a post that it was a squealing capacitor. Does you motherboard have an on-board video chip? I would try removing your 8400 and seeing if its that making the noise. Or just try to boot with as little hardware as possible.
Sorry to bump this again but i found this on the other forum i posted "It's weird, because when I use Prime95 on full load, the sound disappears." Once the CPU cant down clock or slow down it goes away. The same thing happens to me it just a whole load quieter. So its totally a CPU thing. Your best bet is to disable EIST or SpeedStep in your BIOS.
I never though I'd say this but... "Ding, dong, that noise is gone!"
Thanks to all your good advice, here's how I got rid of it:
On my Intel DX58SO BIOS, in the "power" section, there's 4 switches to mess with:
SpeedStep: I left it ENABLED
CPUC State: I left it ENABLED QPI Power management: THIS IS THE ONE I TURNED OFF (DISABLED)
C1E: I left it ENABLED
So if anyone experience this same noise, try switching this QPI thing OFF, may solve the problem.
Just so you know, the noise was coming from an exact place on my mobo, near the CPU.
This image shows the exact source of the noise (negative), located with a cardboard paper towel role (thanks to PDXMark at overclock.net):
Great I'm glad you found the solution. I had a feeling it would of been some sort of CPU clock thing Funny thing is, i have a old Power Mac G4 that has the same sound whenever you do something CPU intense. I guess the problem is universal :-P