I'm wondering if there is any way to hook up some kind of relay or program on the computer then using a serial or USB port to power on the amps. I too have problems with noise during start up (especially on hibernate) and this would be very helpful for me.
The reason you have noise now is because you're using a PCI card that is turned on with the PC as it boots up. Alternatively, with a USB sound card, it's not actually initialized until your already in windows, meaning the sound from before windows boots has no effect on the USB while it does on the dedicated sound card.
You could hook up a manually switch inline with your amps. Then just turn them off when you get out of the car and back on once your PC is booted.