When not caused by a version conflict between IIS and IIS Management Tools, these symptoms are often caused by some corruptions in configuration files under
%WinDir%\System32\Inetsrv\Config. What's in your
applicationHost.config? IIS Configuration Reference:
ApplicationHost.config - This configuration file stores the settings
for all your Web sites and applications.
Administration.config - This configuration file stores the settings
for IIS management. These settings include the list of management
modules that are installed for the IIS Manager tool, as well as
configuration settings for management modules.
Redirection.config - IIS 7 and later support the management of several
IIS servers from a single, centralized configuration file. This
configuration file contains the settings that indicate the location
where the centralized configuration files are stored.
Is your Windows Server 2016 installation a completely fresh installation or is it upgraded from a former version? It's unlikely that the configuration files would be corrupted after a clean install. Is it possible in any way that there was old versions from some previous IIS installation? Does the Date modified of these configuration files correspond your installation date?
As your installation is new, there shouldn't be anything you need to recover. After uninstalling IIS, you could check whether these files still exists and manually remove whole
System32\Inetsrv\Config, if necessary. Then, reinstalling IIS should re-create the files with default settings.