Sure it could be crappy speakers, do you have another pair somewhere, or a pair of headphones, you could dig up somewhere to see if the problem goes away?
It could also be sound card settings, if there are any enhancement/3D/surround gimmicks available in your control panel, kill 'em dead to see if it makes a difference.
I'd still be suspicious of the cabling thing. If you have the polarity reversed on one channel, you'll have reversed the phase so that any sounds coming out both speakers will tend to get cancelled out, and sounds coming primarily from one speaker will seem more pronounced. (This too could be a problem with crap speakers, miswired at the factory.)
Aside from the sound control panel, if you have the sound "enhancer" or other iTunes effects turned on in its preferences, try turning all that junk off too.