What have you specified in your /etc/X11/xorg.conf?
Look into that file and look for Section "InputDevice"
. The main options are Protocol, Device and ZAxisMapping. Here is my config:
Option "Protocol" "IMPS/2"
Option "Device" "/dev/input/mice"
Option "ZAxisMapping" "4 5"
What is yours?
Oh, yeah. As detpenguin mentioned: look for "Buttons" as well. The scroll is considered as two buttons (one down, one up). If you have a three-button mouse you will have to specify 5 buttons for it if you have a scroll as well.