Could be a grounding issue - like if you are daft enough to have one of those little brass extenders, where it shouldn't be... I can say daft enough, because back in the day, my brother and I killed our first PC build doing just that.
Maybe something is building up a charge, or interfering. It's not the sort of thing that you can easily spot, but also - it's very very unlikely that your motherboard or processor are at fault.
I'm thinking that you use on-board sound?
If so - stump up £15 or so, and get yourself a sound card. People assume that on-board 5.1 and lots of ports and lots of fancy doodah's like optical connections counts for something. It doesn't. An AC97 is a turd of a sound card. Seriously, you can spend £15 and get something that puts decent power to your headphones, does proper surround sound if you have the setup, and most importantly sounds much much much much better than any on-board sound card. For the sake of £15, it's a no-brainer - treat your ears and maybe even fix the problem by avoidance

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Health, Ammo, and bacon and eggs!
