It's good to know that the shut-off problem is solved. By rerouting the subwoofer basically your amplifier does not handle the freq below the crossover freq, which is now handled by subwoofer amplifier. It reduces a great deal of load since bass takes a lot of power.

As for the soundcard connection, I strongly believe you are using mono plug. Get the stereo jack as Jeskibuff suggested and I think it will solve the problem. I used to connect my computer from the soundcard to receiver using stereo mini plug at one end and two RCA plugs at the other end and never had such a balance/hum problem. Good luck.