I'm playing Minecraft 1.12.2 in a full-screen mode on my Ubuntu 16.04.
If I switch the keyboard layout, Minecraft switches to a windowed mode. To return to the full-screen mode, I have to press F11.
First I tried to disable all Alt shortcuts in Ubuntu Unity.
Then I tried to change default Alt-Shift shortcut to Ctrl-Shift.
Both ideas didn't work.
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Does this issue persist in the 1.13 snapshots (17w43a/b or newer, but testing on 1.13-pre1 is probably easiest)? The game switched to LWJGL 3 then, and a lot of things about fullscreen differ now.