Just a thought, but very heavy CPU usage by a high priority process can create the symptoms you are seeing of mouse not responding.
Have you tried running system monitor to see wht the usage is?
Do you have any sofware that intersacts between the 2 systems? How about file shares, especially over netbios.
What could be happening is that powering off one machine is causing the other system to spend all its available power searching or trying to do something like recover a file share?????
Anyone else care to speculate on this???
ed for sp