I have an extremely similar setup (Studio 20 v5's bi-amped off a Marantz SR-5003, couldn't justify the price increase for the 6003), and I love it!
Anyway, about your question: Make sure the bi-amped part of the connection (the Speaker C/Rear Surround connections) are correct as well, and make sure you flipped the switch on the back of the receiver to enable the Speaker C setting for bi-amping, although that shouldn't affect this problem...I almost forgot to do that when I hooked mine up.
Besides that, I agree about checking the cable...what kind of cable are you using, by the way? And I assume the computer is a Windows machine? I ask, because Linux liked to reverse my sound card's channels.
Maybe try hooking up some headphones or PC speakers to the computer's audio output (I assume you're just running a 1/8" mini jack to RCA cable from the laptop's front L/R output), and seeing if those work correctly. That would tell you if the problem is with the PC, or the receiver/speakers. You may accidentally have a "reverse stereo" option enabled on the laptop too, either in the aound card's settings, or the media player's settings.