Hi,
no matter of the course_files setting in backup setting, when your course has 'file', 'directory' or 'ims' resources.... using course_files, those needed files to transfer those resources are copied to course_files.
So I guess your courses will have some resources of this type and it's causing "some" files to be copied.
Note this won't be a problem anymore in Moodle 2.0, where each resource is going to autocontain always its own files. But for previous versions, where the course_files is a "shared" (for resources) container, it cannot be done in another way, or you will end with non-working resources after restore.
Closing this as not a bug... thanks for report, ciao 
Hi,
no matter of the course_files setting in backup setting, when your course has 'file', 'directory' or 'ims' resources.... using course_files, those needed files to transfer those resources are copied to course_files.
So I guess your courses will have some resources of this type and it's causing "some" files to be copied.
Note this won't be a problem anymore in Moodle 2.0, where each resource is going to autocontain always its own files. But for previous versions, where the course_files is a "shared" (for resources) container, it cannot be done in another way, or you will end with non-working resources after restore.
Closing this as not a bug... thanks for report, ciao