Didn't notice the amp model was mentioned.
http://www.hyperfi.co.uk/images/MarantzPM6005back.jpg
This is the back of your amp. You can plug your RCA leads into any of the red and white sockets except the ones labelled phono or recorder (Audio Out) and it will work fine. This includes the ones labelled recorder (Audio In).
If that's what you're doing -
1 - Have you got anything else plugged into this amplifier? Does that produce proper stereo sound?
2 - If the answer to 1 is "no", check your speaker cables are wired correctly. (With the amp off, duh) You'll notice you have 8 terminals. This is because your amp can power two sets of speakers independently. If you've wired one of your speakers into the speakers A output, and the other into the Speakers B output, that could cause this problem, since the speakers B output is only used when specifically turned on.
You only need to use the bottom 4 of these to power a set of standard stereo speakers. Make sure you're matching up red to red and black to black. In that image, the bottom right two terminals (The ones on the white dotted background), are for your left hand speaker. The other two terminals on that white dotted background should both go to the right hand speaker.
The top four should not be wired in at all (Unless you're wiring them to a second pair of speakers in another room. And no, having them wired into another set of speakers in the same room is not a good idea and will just sound bad - trust me on this.)
3 - If all of the above has been checked, it's the cable, or the output from your soundcard, or the amplifier has one channel blown. That last one should be unlikely unless you've turned the amplifier to max and blown it up.