car audio problem

I got my system way back in January and am just starting to have problems. Despite what some of you think, I hooked up my amp and two subs to my stock head unit. I like the fact nobody walking by knows theres a system in my car. Anyways, when I turn my car on the bass is REALLY loud. Seriously, you can't hear anything but bass, and it sounds like the speakers will blow. Even with the bass turned all the way down, it's still too loud. After about 2-3 minutes of driving it goes back to normal. WTF is wrong?

I took my ride back to the shop that did all the installation and they wouldn;t even look at it. They said the problem is with the head unit. Are they right? They didn't ven look at my car.