I have this problem as well, with ModernMix 1.2a on Win8.1 Pro x64. It's an infuriating problem that drove me insane until I finally figured out that ModernMix was at fault.
As mentioned previously (THANK YOU!), disabling the overlay is a workaround (NOT a "fix", just a WORKAROUND). After doing this, you will have to rely on only the hotkey to change the window view mode (i.e. windows versus full-screen).
Here is how to disable the overlay:
Once you make those changes, you may then have to restart ModernMix in order to stop the maddening issue with windows not coming to the foreground when they should. The easiest way is to reboot. Short of that, you can:
1. Stop the "Stardock ModernMix" service (you may use services.msc or the service manager of your choice).
2. Manually kill MMix_32.exe and MMix_64.exe ("taskkill.exe /im MMix_32.exe" and "taskkill.exe /im MMix_64.exe", or use the task manager of your choice).
3. Restart the "Stardock ModernMix" service.