figured out how to fix it for anyone who finds this thread later on. Make a file in your home directory called .xmodmaprc and inside it contain this.
Quote:
clear Mod4
keycode 115 = Super_L
keycode 116 = Super_R
add Mod4 = Super_L
add Mod4 = Super_R
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Your key codes might be a little different, use xev to find them out. Then on the first line of your .xinitrc file, add this
xmodmap ~/.xmodmaprc
and vwala.