As a workaround I set my layout switching shortcut to run a script that switches layouts using setxkbmap. I lose the layout indicator applet and it still doesn't fix the problem for the CZ layout, but at least US layout is not affected anymore and Alt+a works there. The script: (setxkbmap -query | grep -q "layout:\s\+us") && setxkbmap cz || setxkbmap us