@Ravi Bhushan , For our issue, we would like to see if our SCOM 2012 R2 is with the latest UR14 installed. If not, we suggest to install it.
Meanwhile, we can also try to clear cache to see if it will help:
- Stop the Helathservice
- Go to C:\Program Files\Microsoft Monitoring Agent\Agent, Rename Health service state folder to Health service state_Old
- Start Helathservice
In addition, please check if there's any antivirus software there. If yes, please ensure all the exclusions are set:
https://learn.microsoft.com/en-us/troubleshoot/system-center/scom/antivirus-exclusions-recommendations
Hope it can help. If there's any update, feel free to let us know.
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