You don't have to power down the hub, just remove power from the SSC. You could unplug the cable from the hub, unplug the cable from the ethernet pigtail or power down the hub, whichever is most convenient to you. I've done them all at one time or another.
I'm thinking that you do not have the correct firmware. Check in the wiki to make sure that you have the latest. There were several variations that came out when the mods were being done.