1-book-per-directory is meant to only import one book per folder.
No wonder it adds only one book.
If you have multiple books per folder, don't use that option.
The primary use of that option is for books that have been in a calibre library before, and are already grouped with OPF/cover/multiple formats.
For new books yo can just drag-and-drop -- unless they are currently organized in folders already.
Do note: You can select a folder full of folders, for the one-book-per-directory option.
For backup, I would suggest using something like FreeFileSync/Synctoy to sync the library folder to your backup drive.