Not sure if you ever found a solution but I was having the same problem and just found a work around.
I found if you turn on a start menu setting that tells Windows to return to the Desktop instead of the Start Screen when all apps are closed will solve this issue you described with Moden Mix.
In Windows, Right click the taskbar, select Properties.
On the Navigation Tab check 'When I sign in or close all apps on a screen, go to the desktop instead of Start"
Press Ok, and now when you close a windowed app nothing will happen (Since you are active on the desktop already)
However, when you startup or reboot, you will not be presented with the Start screen, instead you will start at your Desktop.