Hi,
There are many reasons which can lead to this situation.
Please check belwo articles to fine tune SEPM.
SEPM services take up a lot of CPU and become unresponsive:
http://www.symantec.com/docs/TECH123922
Symantec Endpoint Protection Manager: Javaw.exe and/or semsvc.exe are consuming 100% of the CPU:
http://www.symantec.com/docs/TECH102910
Tuning the Performance of the Symantec Endpoint Protection Manager console:
http://www.symantec.com/docs/TECH105179
Below settings can be helpful to digg out the exact cause underlying the issue.
Monitoring Server Health on Symantec Endpoint Protection Manager:
http://www.symantec.com/docs/TECH122731
Hope this helps you!!