Depois de pesquisar um pouco, os procedimentos abaixo são indicados para solucionar seu problema.
Add apple:badmap option to the "XkbOptions" in the "InputDevice" section in your xorg.conf. The section should look like this:
Section "InputDevice"
Identifier "Generic Keyboard"
Driver "kbd"
Option "CoreKeyboard"
Option "XkbRules" "xorg"
Option "XkbModel" "apple"
Option "XkbLayout" "us,ru"
Option "XkbVariant" ",winkeys"
Option "XkbOptions" "grp:shift_caps_toggle,apple:badmap"
EndSection
This should swap problematic keys under X. If it doesn't help one can try adding apple:goodmap instead.