Hello,
Check these Articles in reference to the Scan Engine :
How to manually update Scan engine with Intelligent updater / Rapid Release
https://www-secure.symantec.com/connect/blogs/how-manually-update-scan-engine-intelligent-updater-rapid-release
Intelligent Updater is not working with Symantec Scan Engine 5.2 installed on 64-bit Operating System.
http://www.symantec.com/docs/TECH98061
Unable to run Intelligent Updater or Rapid Release definitions on a 64-bit Windows operating system to update Symantec Scan Engine
http://www.symantec.com/docs/TECH98065
Secondly, to verify if the Rapid release is updated on the SEPM 12.1, check this Article:
How to update definitions for Symantec Endpoint Protection Manager (SEPM) 12.1 using a .jdb file
http://www.symantec.com/docs/TECH102607
Hope that helps!!