Differentiating between the two Windows keys when defining a Hotkey-combination is not possible. This is due to the fact the when registering hotkeys in Windows, there is no way to make the distinction between the two keys.
It is possible to make the distinction when sending keystrokes, but that hasn't been implemented (yet). I'll implement that in a next version (along with differentiation between the left and right Shift, Ctrl and Alt keys).