Same problem here. Neither the "naturalscrolling" app nor an .Xmodmap "pointer" setting helps with nautilus (or Nemo), but both settings work for other apps (e.g. Chrome, Firefox, ...). Ubuntu 12.04.02 LTS on a Toshiba R850-19Z business notebook (ALPS/2 touchpad).
Same problem here. Neither the "naturalscrolling" app nor an .Xmodmap "pointer" setting helps with nautilus (or Nemo), but both settings work for other apps (e.g. Chrome, Firefox, ...). Ubuntu 12.04.02 LTS on a Toshiba R850-19Z business notebook (ALPS/2 touchpad).