I was just wondering if you solved your problem, because I am having a similiar situation.
I have two amps (one running components up front and one running the sub) and when I turn the volume up the front speakers cut off, but the sub keeps pounding. I have checked the Alpine amp powering the components and the green power light never turns off, but the speakers cease to output sound. When the sound does come in it is clear, but its on for a second, out for 2, on, out, etc... Only at higher volumes (not full blast, but 75% or greater). I currently have 4 guage wire powering both amps, but feel that the 4 guage might be too much for the Alpine, even though it never loses power (according to the green light).
Does anyone think switching to a 8 guage power/ground setup might help solve my problem?