You power the amp through the pc power supply. Problem solved.
Onboard sound and cheap soundcards are pretty notorious for this kind of problem and it's not really cheap or easy to prevent while still using such a device. The way to do it is either with a device that will delay turning the amp on until after your computer is started or will delay (and dampen) the audio connection until after your computer is started. Both devices are available and any car audio expert can direct you to one, but they are more expensive than the following solution:
A good sound card will not do this. I have firsthand experience with Creative Audigy2/NX USB and M-Audio USB devices with the HK amp and they do not pop. It is possible that BMW has changed amp models or something and are now building E46 cars with amps susceptible to this kind of problem, but I doubt it.
If you hear the amp pop even with your soundcard's audio disconnected from it, then we'll have to figure out what's going on with that -- if that is the case you probably have a bad ground connection on your VEN4/SVEN4/Whatever else you use to convert unbalanced to balanced...
I am trying to do the same thing you did with the firewire bridge, but can't figure out how to get it to work. In short I purchased a super slim panasonic cd/dvd rom. I ran the firewire from the computer to my center console where I want to install the drive. I plugged the ide into the firewire bridge, and also plugged the power from the bridge to power on the cdrom drive. Just there is no power nothing is turning on and I have no idea if the bridge is even working. Thanks for your time.
CarPC - 90% Complete -Finally almost all done!