Hello,
Are you using a SQL database? Is this a Fresh Install of SEP 12.1 RU1 MP1 or Migrated from an older version?
If migrated, from which version was the SEPM migrated?
Symantec is aware about this issue. The Issue seems to have been resolved in the Upcoming Version of SEP 12.1 RU2.
Check this Article:
Single risk event notifications generate duplicate emails once every three minutes.
http://www.symantec.com/docs/TECH190349
I would request you to create a case with the Symantec Technical Support on the same.
QuickStart Guide - Create and Manage Support Cases in SymWISE
http://www.symantec.com/docs/HOWTO31132
How to update a support case and upload diagnostic files with MySupport
http://www.symantec.com/docs/TECH71023
OR
To Call Symantec Technical Support :
http://www.symantec.com/business/support/assistance_care.jsp
http://www.symantec.com/enterprise/support/contact_techsupp_static.jsp
Hope that helps!!