On my mixer I've used my master output sockets to plug it into the pc without any problems, I've got a seperate volume control for the monitors which I use so it's not a problem.

Make sure that in the sound control panel (windows -> run -> sndvol32) in the advanced options you've switched to recording and you have the line in input selected.

Anyway the noise could be coming from a loose connnection, make sure all the plugs are firmly seated in their sockets. Make sure as well your decks as grounded on the mixer as well, though if this was the case you would probably hear the noise in the mix.