Problem:

When trying to recconnect, rebuild or reinstall just the application portion of the SEPM, windows authentication fails to connect to the database. The connection information, account permissions, and account passwords are correct. The tomcat error logs show that the domain isnt trusted. DBAs can see that the account connects to the database but goes no further. The error from the installer is that the connection to the database failed (no error code), and it refers you to a troubleshooting document relating to server connections. 

Solution:

Start the Management Server Configuration Wizard using the windows service account needed for the database (run as different user in the right-click menu if you hold down shift). In my case i also needed to grant the account local rights. The database configuration will now succeed.