Skype and other similar programs have code in them to remove the "Static" noise most PC produce when recording, Ive yet to encounter a PC that has no noise when recording raw data from the Mic port, I've have noticed that you get better recordings if you sound card is an add on card rater than mother board integrated , and Laptops suffer from the worst noise.
Could you tell us what kida sound card you have and where it is situated in your PC?, it may simply be to close to a power cable.
you may need to use a noise filter on your recorinds , and aplication i use at my work is called gold wave , its has some noise filters built into it.