[Hampshire] KVMs and Linux v Windows

Hi all

I've touched on this area before but I'm losing patience with it so need a workaround.

Short question: Is there a way to reset a desktop session (via a command) without resetting the machine itself?

Sometimes when I switch (KVM) into an Ubuntu (or Mac Tiger) after a Windows session, the mouse pointer is clearly broken - it doesn't follow the movement of the mouse. I wouldn't mind this if my KVM were mechanical - but it's electronic and provides a signal even when inactive. This doesn't happen switching from one XP machine to another.

When it happens, the only options (that I know of) that I have are:
a) ssh into the "broken" box and reboot it
or
b) VNC into the broken box and reboot it

What I need is a nice command / script which will safely shut down the open apps on the Mac or Ubuntu box and restart the box or something similar leaving the session as it was.

I guess the other option is investigate why this is happening but I've not turned up anything from a cursory google - all my results seem to be to do with virtualisation on Linux boxes.

Thanks in advance as always.

Rob