There can be other sources of noise from computers that will travel down USB cables/analog audio cables to pollute the amp.
On several computers that I have owned in the past, I could hear the CPU churning away through my headphones under certain conditions, and the spinning motors in the hard drives were also quite audible.
Going to an optical connection should eliminate all of this.
You are also correct, the gain of the Crack is bumped up as a consequence of installing the Speedball.
-PB