When you upgrade Search from Ektron 8.60 to 9.00, the following error occurs when EktronSearchConfiguration.exe tries to register the site:  Warning! The current user domain: can't authenticate against the domain: '(domain name)'. If you wish to use a user on the 'dom1' domain then please login as a user on that domain.

When you run the 8.60 installation EktronSearchConfiguration.exe on the same machine using the same domain account, it installs correctly and all functionality is present.

Solution: Install server .NET Framework 4.5

After .NET 4.5 is installed, the site registration process works without incident.