I have two keyboard layouts in my “quick list” or whatever you want to call it. Classical German QWERTZ and the NEO 2 layout. However, Minecraft in non-chat-mode ignores which layout I currently have selected and behaves as if I had selected the first one. When I change the ordering of the layouts in the list, the behaviour of Minecraft changes, otherwise it doesn't. Of course, it should be just the other way 'round.
Is this still an issue in the most recent versions (currently that is 1.12) of Minecraft? If so, please update the affected versions and help us keeping this ticket updated from time to time. If you are the owner/reporter of this ticket, you can modify the affected version(s) yourself.