The problem is that the switch does not correctly handle the mouse wheel protocol (I know ... but don't ask !!). For some strange reason, Windows doesn't care, but Linux goes potty
For what its worth, I occasionally have the same problem with Windows on an expensive Black Box KVM switch at work. Seems to be caused by specific models of motherboards.
I also have the same problem with a belkin four port kvm, but my mouse has no wheel and X is not setup for it and it still didn't work. I wound hooking up an extra mouse so I have two mice on my mousepad I can switch between - wasn't that hard to get used to.
I've also noticed that you can hang a tty console or even a konsole under KDE when switching between KVM ports. Anyone else have this problem?