Depending on the distribution you are using, you may want to see if X is loading the correct parameters in it's config file. Go to /etc/X11 and edit XF86Config-4 OR if you don't have that XF86Config. Scroll down to the pointer section and if you could, put them up here, we could see why it's not loading correctly. Usually all you have to do is make sure that it's using the PS/2 protocol and the correct device eg. /dev/mouse.
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