There's a problem here, and it doesn't have anything to do with KVM switches... My scenario is similar, but I'm not using a KVM. I've got a dual monitor NVidia GT220 video card. Monitor #1 is connected with the DVI connector. Monitor #2 uses the standard VGA connector. When Windows 7 goes into SLEEP mode, all applications are moved onto monitor #1 and I see that when the computer wakes up. SO... this isn't JUST a KVM. Buying a new KVM won't solve the problem.
As a further test, if I cut the power to both monitors, and then restore power to monitor #2 using the vga connector, I see that the computer can only see that there is one monitor connected to the computer.
Surely there is some way to prevent Windows 7 from totally ignoring the sleeping or disconnected monitor (connected via the DVI connector) and resetting where all of the applications are. You would think that Windows wouldn't move the windows before sleep mode starts, or before the computer is completely awake. What gives?
EDIT 1/12/2010: Problem SOLVED.
I did a windows update and installed new NVidia drivers on the box - and the problem has gone away. I can now cut power to the monitors, turn them off, or let the computer go to sleep, and all windows will stay positioned correctly. Perhaps this is just a driver issue.