I have also had problems getting a USB mouse to work through a KVM switch.

I believe this is a limitation of the KVM switch, not a limitation of the mouse or the computer.

My solution was to just have two mice. Everything else but the mouse could be KVM-switched, so I had a second mouse for the second computer.

I believe, also, that there are newer KVM switches that will accept USB mice and keyboards. I think they're more expensive though.