Quick onyx questions

So, I have been using onyx a while, to reset perms and other stuff on my intelimac, but I just put in on my macbook for the first time. When I ran it, I had I THINK the same settings ala, nothing special turned on. And when it finished, my desktop was gone, the HD icons and ALL icons on the DT where gone.

After a reboot I think most of everything was back, but all piled up on the side. Is this a usual first boot/run issue?