Symantec Endpoint Protection is a combination of Symantec Antivirus, Symantec Firewall, and Symantec Spyware. I uses SEP as well. I had to add a few firewall rules to prevent the pops of NTOSKRNL, alex, and a couple of other services that I use.
Since you keep getting popup messages, check the logs and find out the application that SEP does not like and add them to the rules.