this thread should not have been posted in the high end forum....why it was I don't know...
as for your system....the only real reason for turn-on thump (non-carPC related) is a cheap amplifier.
Unplug the RCAs at the amplifier then turn the system on/off a few times. If you still have the noise, then it's the amplifier. If not, plug the RCAs back in, turn the gains down, and turn the system on/off a few times, if it goes away, then you have your gains set too high.
The crackling you've been hearing could also be blown speakers...cause by a crappy amp or improper tuning (turning the gain controls all the way up unjustly so).