my hu has a lil feature that delays turning off the amp due to this //content.invisioncic.com/y282845/emoticons/fyi.gif.9f1f679348da7204ce960cfc74bca8e0.gifNo, I didn't //content.invisioncic.com/y282845/emoticons/wink.gif.608e3ea05f1a9f98611af0861652f8fb.gif But possibly. From my understanding these "popping" or "thump" noises occur when voltage is sent through the remote turn on wire after the amplifier is already on, thus being amplified and creating the noise.
Adding a turn on delay to your subwoofer amplifier, if that indeed is the problem, would solve it.
http://www.caraudio.com/forum/showthread.php?t=405482
I've been going at it for a week now, still a mystery to me.