For best sound you should be connecting the line output of the laptop to the auxiliary input of your stereo with proper shielded cable. If you don't have a line output then the headphone jack with a proper terminating load. I've had good luck with a USB sound adapter that has a line output.
Thanks for your replies. I connected the laptop's headphone jack and the stereo's auxiliary input. The cable is good, I have two and they both give the same results. I'm starting to think there might be something wrong with the stereo's aux input.
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