If the player DOES go into standby correctly when you hold down the top button, then the next thing I would suspect before the player is an issue with the wiring or the amplifier.

First, let's make sure it's wired properly. What are the following wires (from the player harness) connected to?

Blue
Yellow
Orange
Black

What are the following terminals on the amplifier connected to?

Amp remote
Ground
+12v


Most problems with amplifiers making thump noises (or crackling which you say has always been happening) are due to simple miswiring of the amp and head unit. It might also simply be a faulty amp.

One way to prove this is to disconnect the RCA audio plugs from the amplifier, while leaving the power and amp remote signal wires properly connected. At that point, there should be nothing that the player can do to make it thump, even if the player is faulty. All the player should be able to do is signal the amp when to turn on and off. If the amp is thumping with the RCA's disconnected, there's either a serious wiring error or you've got a bad amp.

Finally, check for wiring problems on the docking connector.