Well, according to the manufacturers specs on that decoder, it's equipped with SuperSonic motor drive for silent operation. That said, my original thoughts are now moot.
At this point, and having read your OP again, the naked chassis was smooth and quiet and it became noisy upon installing the shell. That would tell me SOMEthing on the chassis is making contact with the interior of the shell. Double check your installation and pay very close attention as you re-install the shell for ANYthing that may be tight or binding.
Mark.
¡ uʍop ǝpısdn sı ǝɹnʇɐuƃıs ʎɯ 'dlǝɥ
Sounds like an older variety of decoder. The pulse width modulation of earlier decoders worked at a lower frequency that you can actually hear .... well, most of us !
Later decoders, commonly known by terms like "silent drive" operate at a higher frequency that we can't hear .... although your dog may be somewhat annoyed by them. Placing the shell on the chassis is akin to placing that high frequency "buzz" in a speaker box - it just amplifies it.
Some (maybe all) decoders exploit this frequency to dim the headlights. By lowering the frequency of the modulation, it in effect dims the headlight. In all reality, the modulation is actually making the headlight blink - it just blinks so fast we don't see it. When dimmed, the headlight is just blinking a little slower causing it to appear dimmer. I've had a couple decoders that had the modulation on the headlight output so far out of whack, you actually COULD see the headlight blinking !!!
So, in a nut-shell, nothing is "wrong" with the decoder .... it just comes down to how tolerant or sensitive you are to the noise. Myself - it just screams at me and can't deal with it while some of my other operators can't even hear it !