Check
this out.Also check out the troubleshooting part of the KVM switch manual.There's stuff about losing mouse control.
I think that when you log out of the Gnome or KDE session you are freeing up the mouse from that x-session,so that may be the proper procedure.Will have to look into this further.
I have a 2-port Linksys KVM with integrated cables running XP/SuSE 8.1.I will see if I can re-create the problem on that setup.
HTH
lynch