(assigning to gnome-control-center because it has the setting. I'm not sure if whatever it changes is supposed to apply to the XI2 valuators or not...)

(In reply to comment #0)
> Applications like "Files" and "Web" support pixel accurate smooth scrolling.
> With "Natural Scrolling" activated, they keep on scrolling in the usual
> "unnatural" direction.

Does it help if you restart those applications?

See: https://bugzilla.gnome.org/show_bug.cgi?id=705203

There is patch for XI2 to fix this behavioral, however probably not commited yet...

(In reply to comment #2)
> (In reply to comment #0)
> > Applications like "Files" and "Web" support pixel accurate smooth scrolling.
> > With "Natural Scrolling" activated, they keep on scrolling in the usual
> > "unnatural" direction.
> 
> Does it help if you restart those applications?
> 
> See: https://bugzilla.gnome.org/show_bug.cgi?id=705203
> 
> There is patch for XI2 to fix this behavioral, however probably not commited
> yet...

Got a link to that patch/bug where this is discussed?

The patch is at the bug 705203, however it has been committed finally. 

Setting as duplicate, because it works for me. If the behavioral persist, please reopen.

*** This bug has been marked as a duplicate of bug 705203 ***