Hi, 

OS: Windows 10 
When I build emacs from master the super and Hyper keys work as expected. On the other hand, if I build emacs from branch emacs-25 or any emacs 25 pretest both keys don't work. 
These are the git commands that I am using: 

$ git clone git://git.sv.gnu.org/emacs.git 
$ git clone --depth 1 git://git.sv.gnu.org/emacs.git 

$ git clone --depth 1 --branch emacs-25 git://git.sv.gnu.org/emacs.git 

Thanks

Levis