There appears to be a problem with the latest version of the application. It seems to default to use SYSTEM@WORKGROUP rather than the specified user. I had to add NT AUTHORITY/SYSTEM as a dbOwner in order to get the backup to work as it is ignoring my user account setting in the application.
Dear Sam_Smith,
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Thank you and sorry for the inconvenience.
As i understand (but i do not saw any info in changelogs) you turned off sql2000 support in newest version… without declaration of war 
please, could you send me download link to last version with sql2000 support.
Thank you!
Hi anton_kozyrev,
SQLBackupAndFTP creates backups via Standard T-SQL Commands, in the same way as you do it via SSMS.
Could you please try to install the Alpha edition https://sqlbackupandftp.com/download/alpha and check if it works for you?
Also, you can download SQLBackupAndFTP for older .NET Framework v4.6.0 or .NET Framework v4.0.0. The links can be found at the “Download” Download SQLBackupAndFTP - SQL Server Backup Software page under the “Download SQLBackupAndFTP” button.
If you have any other questions, please let us know.
Thank you and sorry for the inconvenience.