To make your mouse wheel work with X you will need change the mouse section X server's configuration file.

  For XFree86®, it's: /etc/X11/XF86Config
  For the X.org server, it's: or /etc/X11/xorg.conf

• Section "InputDevice"
  • Identifier   "Mouse1"
  • Driver   "mouse"
  • Option   "Protocol"   "IMPS/2"
  • Option   "Device"   "/dev/mouse"
  • Option   "ZAxisMapping"   "4 5"
  • Option   "Buttons"   "5"
• EndSection

That should do it!
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