My buddy just installed an Alpine CDA-9853 last night and when he got done the SPL level seemed all jacked up. His stereo is louder than crap at 2 and 3 on the volume control. He is installing this in a 2005 Avalanche and using a box to retain his OnStar functionality.
I installed a POS Pioneer in my mom's car. She had a stock amplifier under the back seat. Took me a bit to figure out it was there, but after some work with the VOM I found out wtf the problem was and bypassed it. Sounds great now. Also sounds like that's your problem. Find that amp, and you find your problem! (I hope)