Hi, I am using ModernMix 1.10 and with the latest Windows 8.1 updates and I'm still having this problem.
In portrait mode, with all apps set to always windowed, I have observed 2 behaviors:
1) 99% of apps (including all Microsoft apps) start windowed briefly then automatically switch to fullscreen with no icon to return to windowed mode in the ModernMix overlay.
2) A very small number of apps stay windowed when first launched (eg. TuneIn Radio and Soda 3D PDF Reader). However, when the app window loses focus, the apps will then autoswitch to full screen mode, but occupy only the middle 1/3 of the screen. This time, the ModernMix overlay will display the window mode icon, but pressing it will not toggle the windowed state.
In landscape mode, the apps appear to behave normally. However, this is still quite frustrating, as the primary reason I purchased ModernMix was precisely to use apps windowed while in portrait mode.
Hopefully somebody will look into this. Thanks.