I have not had that problem. The ~250 MACs (we also unfortunately have) all appear in the Lost & Found bin first and as Groups containing a computer instead of simply computers (very annoying since the group does not disappear after the computer is moved) and then are sorted like all other machines, according to IP address in our environment.
Do you, by any chance, have an "advanced filter" set up that precludes MACs from being displayed within the System Tree? When you use the "search" box on the dashboard, can you find the systems then?
Do you have Rogue System Detectors installed? If so, you could look in that area to see whether the machines are being detected as not having an agent for some reason.
Perhaps the install.sh did not work correctly. Did you create the install.sh through System Tree Actions - New Systems - Create and download installation package? You may get lucky if you try the same procedure again.
Message was edited by: kmcin11 on 12/28/11 7:32:53 PM CST