The problem shouldn't be the headunit. I think its the line converter box (I think that's what is called) that's used to hook up your headunit to the amp. Remember, stock headunits don't have RCA pre-outs, so you'll need this box to hook up to external amps without speaker line inputs. These $hity boxes almost always fail. I know, I had one that failed and everytime I accelerated the subs would lose power. I finally upgraded to a headunit with 3 pre-outs and I have complete control of my system. I can control how much bass my subs get and can even fine tune speakers individually from my headunit.

Check this box first before you blame the problem on your stock headunit.