If you are seeing over 200 clients with the yellow dot, I would suggest the following:
1) Upgrade the master server to the latest SEPM (now = 12.0.2 RU2)
2) Run a repair from add/remove on the SEPM server.
3) You should be running the SEP firewall and not the windows firewall.
4) Test clients (a few by upgrading them to RU2. Make sure you do NOT install SEP clients using the CD. Only Push install from the master.
5) Check the event logs on both the master and a few of the clients.
6) Make sure clients are running SEP firewall, not Windows.
7) Also, try on one client uninstalling SEP client completely and then get a copy of cleanwipe from support and run that. Make sure all folders relating to SEP or Symantec or liveupdate are gone. If you have netbackup, Backup Exec, or other Symantec products, remove them too. Get client clean.
8) push install the client
9) Check your NTP policies. Are you blocking something you should not block?
If this affects 200 clients, either you have a bad package or something is not right on the master SEPM. Make sure you are not running UNMANAGED clients (installed from the CD). Also, make sure you did NOT install the client on an image (GHOST) unless you are going to use the Sylinkdrop utility for fix the communication parameters.