After update from virtualbox 3.x to 4.x the scroll wheel of my mouse stopped working - just behaved as a three button mouse.

Newer versions of debian no longer have an xorg.conf file - since it's not normally needed.

After some searching I found that it has a config loading directory /usr/share/X11/xorg.conf.d/ and virtualbox had added a 50-vboxmouse.conf there.

I changed this file from

Section "InputClass"
        Identifier      "vboxmouse"
        MatchDevicePath "/dev/vboxguest"
        Driver          "vboxmouse"
EndSection

to

Section "InputClass"
        Identifier      "vboxmouse"
        MatchDevicePath "/dev/vboxguest"
        Driver          "vboxmouse"
        Option          "Buttons" "5"
        Option          "ZAxisMapping" "4 5"
EndSection

and I have my scroll wheel back.