Ok what you have to do is this.
Uninstall the system center from your master server (the one with the blue arrow which you see when you go into system center, by default the first server you install the system center to.
Once you uninstall the system center you will have to reboot.
Now install the new system center for version 9, install this only, no other options, reboot.
Now go into the system center, go to server rollout and upgrade the NAV server client running on this and any other servers you have, the upgrade is pushed out during the process (you have to choose update) and then you have to reboot this and any other servers you updated to version 9.
Now you have to go around to every workstation, uninstall the NAV client/reboot, and install the new client, either manually or push it out.
AM