i had an avalanche that did that... WAY later i found out the root to the problem was my sub preout from my HU... i dont knwo if its your problem but it could be somethign causing it before the sub....
WHEN THE VOICE COILS GET HOT IT INCREASES THE IMPEDENCE AND THAT WOULD MAKE THEM QUIETER BECAUSE THE AMP WOULD PUSH LESS WATTS INTO THEM. I SOUNDS LIKE THAT'S NOT THE PROBLEM THOUGH. CHECK THE GROUND.