I can try it as a solo USB 2.0 device, I'll edit this post later today with the results. In case anyone is wondering, I'm using the Asus Maximus VI hero.
EDIT: Still get about 3 crack/pops with 2.0 as the only device plugged in. With USB 3.0, and headphones plugged in, 1 click sound, the same as when you go into X7 control app and change from speakers to headphones or vice versa. With USB 3.0 and no headphones plugged in, no clicks on startup. It looks like the X7 defaults into speakers mode on startup, and then one click sound occurs when it recognizes and switches into headphone mode. This makes sense to me, and hopefully others can confirm this.
This is with a hard on/off cycle with the X7. I am going to now see what happens when you shut down the PC, but do not turn off the X7 and instead let it go into its standby? mode.