File and folder security permissions are not copied

To copy file security permissions: modify your profile, enable Expert mode (via the Click For Options button), go to Copy/Delete -> Folders settings page, and tick the ‘Copy sub-directory and file security permissions’ option.

Note that file & folder permissions are only copied when the file or folder itself is copied. This means, for example, if only the security permissions change, but not the file itself, then the permissions are not copied across (because the file itself was not copied).