My CarPC does the same thing. Weird.
Why do I get engine noise when the laptop is off and none (or very little) when it's on. When I start my car I get a very loud whine, then as windows boots and takes control of the sound I hear a loud pop and it goes away. I tried to ground the audio cable and found that it does the exact opposite, when the laptop is off, no sound when it's on, sound.
Yep same here.
I just put in a toggle switch that keeps the amps off until windows boots up.