Dual subwoofers are quiet unless the balance is set off the to right or the left side?

I have two sub-woofers in my trunk and after installing an LOC and AMP I noticed that the subs were REALLY quiet. The first thing I did was play around with the Right and Left balance of the overall car audio through the stereo. I instantly noticed that the subs would start hitting really hard when the balance was set off to the left side or set off to the right side but never hit hard when balanced in the center. I want to know how i can get the sub-woofers to play loud on their own with out compromising half of the audio in the car. Is this a phase issue? Is my LOC not wired correctly to the rear speakers?