In Ubuntu with a PS/2 mouse, the scroll wheel stops working when you switch away with a KVM switch. I found some good instructions for fixing the problem on 8.04 here.
There are a few minor changes for 9.04. Here are the steps:
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Add the following to /etc/modules
psmouse
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Create /etc/modprobe.d/psmouse.conf and give it the following contents:
# Make my mouse work with KVM options psmouse proto=imps
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Finally, reload the mouse module:
# sudo modprobe -r psmouse # sudo modprobe -a psmouse