The automatic renaming feature only happens once: when you first connect to the data. If you have added new fields to a data source, and you have a workbook that is already connected to that data source, then refreshing the data source will bring in the new column with the database name. See New Database Fields Added To Existing Connection Without Friendly Name
If that is the behavior you are seeing, you will have to create a new connection to the data source to get Tableau to rename all of the fields.
If you are seeing this occur in a different circumstance, will you please describe the steps taken to get into the state where fields are not automatically renamed when making a new data connection?