Note that the KVM Switch (typically) implements an intermediate "device" for
the mouse so that when you are switched away to the other machine, the first
machine is still "talking to something".
This has the less-than-desireable effect of causing the mouse device "inside
the switch" to act as a largest-common-denominator. Consequently many of
the special features and peculiarities of your real device may not be
accessible to your computer.
A particular, and bette-documented, example of this can probably be found by
trying to hook up a "new-fangled" keyboard (with the media control key
cluster across the top and such) to your windows box. When the keyboard
drivers cannot find the special buttons and you call the KVM switch vendor
they will promptly tell you about how all those hot extra buttons are not
supported with their product, have a nice day, good-bye... 8-)
The same things go four your mouse, but are not as well documented and
accessible to the KFM help desk weasels.
You should find that if you select a "much more generic" mouse configuration
"everything works fine".
Some newer windows drivers "look past" the switch and activate the mouse
features anyway.
Regardless, if your "other" computer is initializing the mouse through
voodoo and dark magic to increase the reporting (baud?) rate and such, when
you toggle to the Linux box you will see all sorts of unhappiness. The
inverse is also true, if the windows driver is expecting
fast-and-feature-full and the side trip to Linux has set things back to
mundane, the return to Windows will be "exciting"
(My optimal configuration that saves heartache)
2-Port plasma flat panel
DVI port connected to my primary use machine
VGA port connected to my KVM