So you did not alter the power wiring in any way? Did you respect hot/neutral when you wired things up (sounds like you clipped the end off, maybe)?
On a different topic, are the new speakers the same rating (8ohm/4ohm) as the old ones? Seems odd that you'd have no problems with your ipod then get this behavior when using a PC (again, seems more like a ground loop), but who knows.