We've actually added a HotKey in the latest 4.1.0 Beta versions that will prevent the game windows from being minimized when losing focus, so perhaps this will help solve both issues :)
Just set a key combination for the "Prevent Window Deactivation" HotKey and apply the settings. Then, before you launch the game, press the key combination. After you're done playing the game, press the key combination again to turn it off.
Please let me know how that works out.
Thanks!