I've installed SSM Agent (2.2.607.0) on Windows Server 2012 R2 Standard instance with the EC2 Config (4.9.2688.0). After installing it, i cannot see the server on the Managed Instances screen. I did the same steps on other servers (Windows and Linux) and it worked.
Tried to uninstall the EC2 Config, reinstalled it again with no luck. Tried to install a different SSM Agent version (2.2.546.0) with no luck also.
Any thoughts?
The agent is installed, but the instance still needs the proper role to communicate with the systems manager. Particularly this step of Configuring Access to Systems Manager.
You should review the whole configuration guide and make sure you have configured all required roles appropriately.