On some systems, Windows likes to shuffle applications around whenever the monitor configuration changes. The easiest way to get around this would be to assign key combinations to the "Save Window Positions" and "Restore Window Positions" functions on the Settings > Functions tab. Then, you can run the Save function before switching profiles, and the Restore one after switching.

This can be scripted too. I've put a script called "Save Window Positions, Load Monitor Profile, Restore Window Positions" in the repository. You can grab it by clicking "Download Scripted" on the Settings > Functions tab. You just need to update the script to point to your Monitor Profile name, and then give it a hotkey.

Hope that helps!