Unfortunately this is due to Microsoft launching the store in the background in hidden mode on login.

ModernMix only applies the settings on app launch and so if you run the store again it will simply show the hidden store vs launching it again.

If you go into the task manager, you will still see it running after you close it down from full screen mode - close it from there too, and when you reopen it, it will open in a in a window and continue to do so for some time (probably while it remains cached).  After a while, it will go full screen again and you have to repeat the process.

Hope this helps!