The Logitech K800 illuminated keyboard is pretty cool but it has a weird Alt/Windows key behavior that is impervious to changes in the standard Keyboard preferences pane. I downloaded DoubleCommand to simply swap the keys more permanently and it’s been working fine.
Being that I’m a clever girl and decided I liked the “feel” of the Windows key better than the flat feel of the Alt key, I swapped those physically on the keyboard.