Hello,
What version of SEPM 12.1 are you currently running?
This was a known issue with earlier version of SEP 12.1.
Please migrate SEPM and all the SEP clients to the Latest vesion of SEP 12.1 RU3 as it resolves the issue -
Symantec Endpoint Protection client fails to report reboot status to Symantec Endpoint Protection Manager after upgrade to 12.1.2
Fix ID: 2871345/3069464
Symptom: The Symantec Endpoint Protection Manager console shows "Restarted Required" as "No" for clients that have not restarted after the upgrade to 12.1 RU2. The deployment status in the Symantec Endpoint Protection Manager console displays the message, "To provide complete protection Symantec Endpoint Protection requires this computer to restart." The Symantec Endpoint Protection user interface on the client also shows that a restart is needed.
Solution: Modified the upgrade process to send the latest opstate data to the Symantec Endpoint Protection Manager server.
Reference:
New fixes and features in Symantec Endpoint Protection 12.1.3
http://www.symantec.com/docs/TECH206828
Check this Thread with similar query -
https://www-secure.symantec.com/connect/forums/after-restarting-pc-still-remains-previous-version-and-says-it-needs-be-restarted
Hope that helps!!