I finally got it to work!
I’m using canadian french keyboard, so I put the OSX “Move focus to next window” shortcut normally “cmd+`” to “cmd+/” so it would be at the same place as a regular keyboard.
The default in Atom for “cmd+/” is toggling line comments and I couldn’t change the key-binding of toggle line comment in atom (don’t know why). So I changed the “toggle comments” in the edit menu via “OSX -> System preferences -> Keyboard -> App shortcuts” to something else (ctrl+q). and changing window works once again!