Driver

I just thought of another question to ask you. How are you sending signal from your head unit?
Are you using RCA outs (from the head unit) straight to your theater amp < to > your sub amp?
OR are you using the amplified speaker outputs (IE: regular speaker wire outs)


EDIT: try turning your bass down on the head unit and let the sub do the low end work. It may be that you're clipping into protection mode because of the low end. Low frequencies can carry alot of power and it may be possible that that your first amp (running your smaller speakers) may be clipping out. Which would in turn clip out the following (sub) amp.
Personally, I would try and run as many of the smaller (IE: front door, rear deck speakers) off of the head unit itself and just amplify the sub. I know you may posssibly have some really good front and rear speakers, but they don't need SUPER power. even if you've got some MB quarts or Fosgates you really only need to give them about 50-75 watts a piece. Let the sub do the thump.
And to add to SQ's idea it is never a good idea to run your amp wide open-(all the way up.)
Try a couple things and see what works, and keep us posted on what you figure out. I'll respond whenever I check my email. Good luck with it, and don't cross your speakers poles (put positive bridged with negative) to force a cutoff again, you can only do that a few times, if not once, before you damage the speakers