Hey Rob, there's nothing left, you've just ruled everything out.. software, input jack and cable!! I don't see how both (audio) line-in jacks could be faulty, but I guess it's possible. The other two a mono in any case.
I think you should double check the above again to be sure. I'm still convinced there is something wrong with that audio cable your using. Possible break somewhere, maybe. I would try another just to be sure.
If all else fails, you may want to try a device like this
C-Media 7.1-Channel 3D USB External Sound Pocket C-Media A-CM106 (which you can buy very cheaply from somewhere like e-bay).
EDIT: Marked as Answered.