It seems that the separate layout has been replaced by a variant, which is
more logical. The right configuration is:
Section "InputDevice"
Identifier "Generic Keyboard"
Driver "kbd"
Option "CoreKeyboard"
Option "XkbRules" "xorg"
Option "XkbModel" "pc104"
Option "XkbLayout" "us,cz"
Option "XkbVariant" ",qwerty"
Option "XkbOptions" "grp:shift_toggle,grp_led:scroll"
EndSection
(note the comma in the variant specification)
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