Do you have a cell phone in the car when this happens? If so, is it plugged in for charging through the cigarette lighter?
On one of the Droid forums, someone complained that he had a brand new phone and charger and when he went to charge through the cigarette lighter, he heard extraneous noises through the audio system. Although the designers of sound systems try their best to avoid this sort of thing from happening, there are occasions when issues like these appear.
There are sometimes 'band-aids' you can put into your system to 'fix' issues like these but many people don't want to because they think systems should be perfect when purchased.
I was wondering if maybe your system had a cell phone in it. It doesn't have to be plugged in to have weird noises come out of your audio system. On my home computer system, I have a 5.1 speaker configuration and when I set my Thunderbolt near my keyboard and mouse, the audio system picks up crosstalk through the air waves and I hear a strange buzzing sort of noise come out of the speakers. I simply move my phone two feet to the left and the noise goes away. In a vehicle, it might not be so easy to troubleshoot but it was pretty obvious on my home computer since I've had things like this happen in the past with other cell phones.
If you don't have a cell phone in the car, maybe a little more detail about other conditions could be helpful...?
Good luck figuring out what's wrong. These issues are definitely annoying.