How is the system wired? The reason for this question is that when I had a fine car system (years ago), the bass would change dramatically when the fader was set differently. I don't remember the EXACT details, but it was something like this: If I faded more to the front or the back, the bass was amplified a great deal. This had to do with a way of wiring for two fronts, two rears, and a subwoofer that wasn't exactly "by the book" because the head unit technically wasn't set up for 4 speakers (as I recall). It worked, and allowed 4 speakers to play, but the fader really screwed up the sound. I never got a satisfactory explanation for this (meaning an explanation that I could understand), but apparently the technique used was quite common for installers at the time to "cheat the system" so to speak.
So, the point of this is.....could it be that there's a quirk in the way that your system's installed? It sounds odd, but I can attest to the fact that there are installation techniques that cause non-linear deviations in tonality.....if that makes any sense.