Just add my confirmation that I have no issues with GUI bindings on either MacOS Sierra with emacs 25.2 and org 9.0.7 or under Linux with Ubuntu 17.04 (same emacs and org versions).
1. You use emacs -q and just load the version of org which is bundled with emacs?
2. you use emacs -q and just load latest org from elpa?
#+BEGIN_SRC emacs-lisp
(when *is-a-mac*
(setq mac-command-modifier 'meta)
(setq mac-option-modifier 'none)
(setq dired-free-space-program "gdf")
(setq insert-directory-program "gls")
(setq default-input-method "MacOSX")
;; Make mouse wheel / trackpad scrolling less jerky
(setq mouse-wheel-scroll-amount '(1 ((shift) . 5)
((control))))
(dolist (multiple '("" "double-" "triple-"))
(dolist (direction '("right" "left"))
(global-set-key (read-kbd-macro
(concat "<" multiple "wheel-" direction ">")) 'ignore)))
(bind-key "M-'" 'ns-next-frame)
(bind-key "M-h" 'ns-do-hide-emacs)
(bind-key "M-`" 'ms-do-hide-others)
(use-package applescript-mode
:ensure t
:mode ("\\.applescript" . applescript-mode))
(use-package osx-plist
:ensure t)
(use-package osx-trash
:ensure t
:config (osx-trash-setup)))
#+END_SRC