When using a global keyboard shortcut (I use Win+F5 through Win+F8) to control a media player (I've tested JuK and DeaDBeeF), Minecraft goes from fullscreen to minimized for some reason. Every time!
Environment
Arch Linux x86_64, KDE Plasma/KWin 5.8.3, jre8-openjdk 8.u112
Please check if the latest development snapshot 17w43b fixes your issue.