While providing support at a customer, I encountered a strange issue with the SCOM agent installations as shown below:

Upon investigation the findings were as follows:
The usual workaround is to delete the following three Registry Entries:
- HKEY_CLASSES_ROOT\Installer\Products\Microsoft Monitoring Agent ID (D996D247BE65CC940AA413D70EF113DC)
- HKEY_LOCAL_Machine\SOFTWARE\Microsoft\Microsoft Operations Manager
- HKEY_LOCAL_Machine\SOFTWARE\Microsoft\System Center Operations Manager
Usually
after deleting the above entries the installation works, however agent
installations from the console as well as manual installations still failed
with the above error, even after server reboot.
The successful work around I attempted is below:
MOMAgent.msi /qb NOAPM=1 USE_SETTINGS_FROM_AD=0
USE_MANUALLY_SPECIFIED_SETTINGS=0 MANAGEMENT_GROUP=managementGroupNameHere
MANAGEMENT_SERVER_DNS=MS Server Name here FQDN MANAGEMENT_SERVER_AD_NAME=MS Server
Name here SECURE_PORT=5723 ACTIONS_USE_COMPUTER_ACCOUNT=1
AcceptEndUserLicenseAgreement=1
After running the command in elevated command prompt the install was successful. Next I identified that the server did not show up in the Management Console. I then checked the configuration of the Microsoft Monitoring Agent under Control Panel and identified that the Primary Management server was showing “Not Available”.

Only once I deleted the entry and re-added it manually with changes applied, only then did the agent show up in the SCOM Console for approval under pending management.