Posted here https://moodle.org/mod/forum/discuss.php?d=228682 without response so far but have been successfully restoring courses into our test 2.4.3 (Build: 20130318) without legacy files appearing by following instructions here http://docs.moodle.org/24/en/Legacy_course_files#Can_you_migrate_a_course_from_1.9_to_2.2B_and_NOT_end_up_with_a_legacy_files_repository.3F.

Recently updated our new Moodle installation in preparation for the summer to 2.4.3+ (Build: 20130425) and following the exact same process legacy files have started re-appearing.

Legacy course files repository is disabled at site level and the 'legacy course files in new courses' option is unchecked.

In 2.4.3

1. Create an empty course

2. Restore the 1.9 backup into it using 'Delete the contents of this course and then restore' option

3. Keep the 'Overwrite course configuration' option set to NO

4. The course restores without legacy files.

Repeat in 2.4.3+ and legacy files appear.