I am unsure off the top of my head, but here is what I know.
if you have set up your CD to run on boot, then unfortunately it will appear at boot.
There are some settings that can be adjusted so that the dock will disappear when not hovered by, and I know there is a setting that will allow th edock to vanish upon clicking the mouse away.
Let me look into this when I get a proper opportunity, as it is now, I am doing a dead install of Vista, 7, and Ubunutu to a new drive, and taking my time and doing it right, so unfortunately, I am in the OS stage still and have yet to re-install CircleDock.
Let me know if you are having issues getting the settings to work right, and I will expedite in your assistance