The website that I am referring you to specializes in noise prevention in your sound system. If you click on the link and scroll almost down to the bottom of the page there is a section specific on ignition noise through your stereo.

http://www.termpro.com/articles/noise.html

Hope that helps!

your car has a bult in sound supresion sys. i think you have a short in you sterio sys . be it in the head unit or in the harness

You most likely have a short or unshielded wire that is allowing interference or electrical noise to be transmitted.  It is in all speakers, or just one in particular?