I had exactly the same issues when I combined display switching with workstation switching on my MCPro (+ Gefen 2x1 DPKVM) .
I'm using a small program called "Display Maid' which basically moves your open windows to a pre-programmed arrangement when it senses a change in displays configuration.
Hopefully "Display Maid" is what you'r looking for?
http://www.funk-isoft.com/display-maid.html
Niek/ Amsterdam