by Emma Richardson.
This is not a problem - it is doing exactly what you told it to do. Originally you were storing backups in the course backup area - then you changed settings and told it to store in a folder. The new backups are in the folder - they are not accessible from the course backup area. The backup in the course backup area is the last one that was created there - prior to the changes you made.
If you want new backups in the course area as well, you need to select Specified directory and Course Backup Area. This will give you double protection.