In the mouse InputDevice section of your XF86Config file, make sure the following two lines are present:
Option "Buttons" "5"
Option "ZAxisMapping" "4 5"
The 5 buttons refers to the left and right button, the middle wheel button, and scroll up and scroll down on the wheel. I know, seems weird but that's how it is.
If you have more buttons, then alter those parameters accordingly.
My Logitech MouseMan has a thumb button as well (making 6 buttons), and I have to use the xmodmap command to correctly re-map the actions associated with each button.
This is definitely one area where Linux/XF86 could have a better out of the box experience.