The first thought that pops into my mind is that the fan of your Graphicscard is messed up. You did however say that you could play some games for hours without the sound becoming a problem. That seems to rule out the fan on your gp.
Open your case and leave it open. Once the sound starts to rise again try looking at wires touching one of your vertical fans (like the one on your cpu), the chances of one of the wires touching your horizontal fans is low since they are all blowing down, and wires tend to fall down just like anything else exposed to gravity. Wires touching fans tend to make huge noiselevels and could have been created when you swapt gfx cards and toucht the wires.
If this is not the case then your cpu heats up and you have a cool and queit system integrated in your mobo bios. Check your Bios book that came with the mobo or the manufacturers website.
If that is still not the case then post again and we will see from there.
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