Maybe it's the
PHAT noise //content.invisioncic.com/y282845/emoticons/smile.gif.1ebc41e1811405b213edfc4622c41e27.gif
Honestly though, What the hell. I can't find it's S/N anywhere. You guys got that? Excelon likes to have an S/N of 98 or better, but I can't find it for this unit, and Kenwoods home site is as detailed as fingerpainting.
Oh ya, thumping seems to be associated with bad RCA pre-outs, RCA line ground issues, ground loop isolation, and crappy built decks. Also, when turning the car on, it could be the external amplifier does not have the right circuitry on the board to avoid the power-up thump, but I'm not sure if that is what you are talking about.
I blew the RCA-preout grounds off the deck and it would thump and makes all sorts of noise even with the car off. Try doing this:
http://www.caraudio.com/forum/showth...ternator+whine
But, before that make, sure to isolate your issues.
Best way to do this is to leave your amp and remote wire together, so that it powers up with your system, but disconnect the RCA's from the rear of the deck. If your gains are where you want them, and you still hear noise, it could be the amp or the RCA's.
Try listening close to each speaker to verify whether or not it is one specific speaker that is worse or not.
Then, disconnect the RCA's. If the noise is still existent, then you either have the Gains to high or your amp is not up to par with your own listening standards.
If it does seem to be the deck (which your description leads me to believe) try to find a good bolt that you can run a small 16 gauge wire too. Take 2 or 3 runs of 16 gauge (I just split the speaker wire I had left over from an install) and wrap them around the RCA pre-outs much like the OP in the above link did.
If you have room, plug in your RCA's before you touch that ground wire to the RCA-pre-outs, turn on the deck. Then touch the ground to your RCA's and see if the thump/noise dissapears as you operate your deck. If it does, your solution was eliminating the ground loop from your deck to the (probably still factory) Ground point that was provided.