Is the noise there before the recording? Could be a noisy mixer or pre-amp. For example I have a cheap desk and the pre-amps are really shitty. If I turn the pre-amps up there is an audible noise.
Maybe check your cables too.
I doubt the noise is coming from the sound card - but there is a chance. Do you have any other cards next to the port that has your sound card (i'm guessing it's a PCI sound card by the way)?
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