This problem is likely one of the most annoying, yet persistant problems in Linux, one of those things that makes you scratch your head and wonder why it seemingly cannot be repaired. In truth, it's an X problem, but you'd think most distributions would have chimed in by now.
In the /etc/X11 directory, you have a file named XF86Config, or XF86Config-4, or similar. Use an editor to open the file (if you have a Unix background, vi or emacs will work, but for most people, the 'nano' or 'pico' editor is easier to use.
Basically, the config for X (the windowing system) needs the mouse set as 'IMPS/2', but the automated config files set it as 'Imps/2'. Don't ask me why, but my guess is that Unix needs the alternate item.
so, your XF86Config[-4] should look similar to this:
Identifier "Mouse1"
Driver "mouse"
Option "Protocol" "IMPS/2"
Option "Device" "/dev/psaux"
Option "ZAxisMapping" "4 5"
Of course, this is for ps/2 mice, usb mice might have a similar problem, but I don't have one available at the moment, sorry. The ZAxis part controls the scrolling, by the way. This holds true for all PS/2 mice from most manufacturers, too, including logitech and generics.
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