Correct me if I'm wrong, but when you click somewhere with your mouse, it should actually effect that spot... Well.. for some odd reason my mouse is clicking about 4 pixels to the left of where the mouse is on this particular system lol

Here's my mouse device calls in XF86:
Section "ServerLayout"
Identifier "XFree86 Configured"
Screen 0 "Screen0" 0 0
InputDevice "Mouse0" "CorePointer"
InputDevice "Keyboard0" "CoreKeyboard"
EndSection

Section "InputDevice"
Identifier "Mouse0"
Driver "mouse"
Option "Protocol" "auto"
Option "Device" "/dev/mouse"
EndSection

Section "InputDevice"

Identifier "Mouse"

Option "Protocol" ""
Option "Device" "/dev/mouse"
Driver "mouse"
Option "Emulate3Buttons"
EndSection

It could be a problem with your display setup, although kind of unlikley. Make sure your resolution, desktop size, and such are all set correctly.