Since the upgrade to Gnome 3.4, applications with smooth scrolling have not respected the xinput pointer button mappings.  I use the natural scrolling app and when I turn it on, my xinput button mapping is as follows:

>>> # Note the reversal of 4<->5 and 6<->7.
>>> xinput get-button-map 11
1 2 3 5 4 7 6 8 9 10 11 12

Even though the scroll buttons for vertical scrolling (4,5) and horizontal scrolling (6,7) are reversed, the scroll directions for smooth scrolling applications (like gedit and system monitor) is not.  For applications that haven't been upgraded to use smooth scrolling (like chrome and gnome-terminal), the button mapping works as expected.

I'm using Gnome 3.4.1.  For other reports on this issue, see:
https://github.com/cemmanouilidis/naturalscrolling/issues/28
https://bugs.launchpad.net/ubuntu/+source/gtk+3.0/+bug/966237