I would suspect that you have alternator whine and probably ignition noises being picked up.Originally Posted by Nokia6600
These problems are because of ground loops being created when you connect your head unit to your computer setup.
THese can be fixed, the quickest way is with a ground loop isolator (Transformer) see the following link:
Not the best quality, but it is a quick way to solve a problem.
The best way to solve your problem it to modify the ground on your head unit, computer-power supply so that they will be grounded at the same ground point and make sure that all your ground points are clean and making good contact. The same goes for your amplifier, verify its ground connection to the chassis of your car.
The next problem you might encounter is the ground from the Antenna, there again, check the ground connection.
As a rule of thumb, the more units (Hu, processor, car computer, amplifier) you put in a car sound system, the more chances of getting ground loops and noise. Those can be solved but you need to be patient.