I too had the repeated:
SEVERE: Unknown Exception in: com.sygate.scm.server.task.PackageTask
java.lang.NullPointerException
in scm-server-0.log
Some groups would not update virus definitions and the Policy Serial Number + Policy Date remained unchanged despite recent policy changes. If I created new groups they would have no Policy Serial Number and no Policy Date and they also would not show up as hexadecimal folders in "C:\Program Files (x86)\Symantec\Symantec Endpoint Protection Manager\data\outbox\agent" (the groups in question also would not change modified date in this folder).
I tried everything else and ended up with:
Stopping services (Symantec Endpoint Manager and Symantec Embedded Database) and restoring the "C:\Program Files (x86)\Symantec\Symantec Endpoint Protection Manager\db" folder to a point in time before the last "Policy Date" on the groups in question (although dbvalidator said the old db was ok).
After that everything worked again.
Since it was also complaing about two old Symantec Installation Packages (hard to find the media for those old versions) I also had to import those two old installation packages and delete them again (import form the SEPM\Packages folder on the installation media and point to the SAV32.info file and name it "Symantec Endpoint Protection version 11.0.2010.25 for WIN32BIT" which name can also be found by opening the SAV32.info file in Notepad)