Does Backer get confused by similar short file names for MS-DOS?
Not Backer, but Windows. This is one of the nastiest bugs in Windows. The automatically assigned 8.3 file names of identical long file names in different directories are not necessarily identical. Conversely, identical 8.3 file names in different directories do not always belong to identical long file names. Unfortunately, this puzzles Windows’s internal search functions – there is nothing Backer can do to straighten this out.