OK, you need to do ONE THING! And that's to call Roger Sanders on Monday (after sending him an email with a link to your system page) and ask HIM what the problem is.
He designed your speakers, amps and preamp, and can give you a pinpoint diagnosis. It sounds to me like there is something (probably the preamp) being dynamically overloaded by the CD player (they always have more output than other sources) and there should be a way to internally select a lower global output from the Esoteric X03-SE. But don't take my word for it, Roger will know for sure.
http://www.sanderssoundsystems.com/
He designed your speakers, amps and preamp, and can give you a pinpoint diagnosis. It sounds to me like there is something (probably the preamp) being dynamically overloaded by the CD player (they always have more output than other sources) and there should be a way to internally select a lower global output from the Esoteric X03-SE. But don't take my word for it, Roger will know for sure.
http://www.sanderssoundsystems.com/