Hi Dame,
This problem could be caused by many things.
The 1st obvious thing to check is that your HiFi is ok [you've probably checked this already] by playing a regular CD.
I suspect that the problem is caused by the connector lead from hifi to PC. The connectors used are notoriously shoddy so make sure all your plugs are pushed fully home.
Oh! and check the lead is stereo I presume one end has two phono plugs which connect to the hifi but check the mini jack on the other end it should have three distinct sections at the end, the almost-spherical tip, a thin band of black insulation, a thin band of metal, another thin band of black insulation, then the rest of the metal "prong" if there's only one ring of black insulation the it's a mono plug - go buy a stereo one.
Play a record and open your recording prog and somewhere there should be an input level display ie a double bargraph showing left and right channels both should be "bobbing" up and down. Record a track save it makeing sure u r saving a STEREO .wav then display the wav. The .wav should be clearly shown as l&r waveforms one above the other. If u r not getting a stereo .wav then go back and check everything over again.
Come back and tell us how you got on.