Oracle has two different ways to identify the "named" database namely using the Service Name and using the Service ID (SID). WebCenter systematically uses the SID.
In WebCenter 12.1, running the database scripts automatically during the installation was introduced. For Oracle, this utility contains a bug as it uses the SID as the Service Name. This means that running the database scripts automatically from the WebCenter Installer works only if the Service Name and the SID are exactly the same.
Running the database scripts fail, when running them automatically from the installer or using the updated_db.bat file from Server Tools (the new way as of WebCenter 12.1).