This article describes why FortiAuthenticator Agent for Microsoft Windows does not display any domain.
Under Two Factor Authentication > Configure, no domain is seen. Even Windows 10 client machine is added in domain, FortiAuthenticator Agent for Windows does not display any.
The reason is that FortiAuthenticator Windows Agent is installed using a local account, instead of using a domain administrator.
FortiAuthenticator Windows Agent should be removed from Windows machines and should be installed from scratch using a domain administrator account.