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This is because when installing the software, when choosing SQL authentication "Windows Authentication" was selected.
To be able to using the FQDN and connect to the console remotely the database must be installed using "SQL Server Authentication" using the SA account.
You will need to uninstall the software and then reinstall pointing to the exisiting database but connecting using SQL Server Authentication and the SA account.
All profiles, license information etc is all stored in the database so no information should be lost. If you have made custom changes to the file BinaryTree.DirSync.Exchange.exe this will be over written so a copy of this file must be taken.
If you do choose to reinstall then you must ensure that you have a backup of the SQL database and if the DirSync server is a virtual server then take a snapshot in case a roll back is required.