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This isn't strictly a key-bindings problem, other events also cause problems. 
I've patched ScriptBinding.py and repacled run_module_event that causes the original, now renamed, method to be called a little why later. This change doesn't fix the issue but makes it even worse: even the menu no longer works.
 def run_module_event(self, event):
 self.editwin.text_frame.after('idle', self._run_module_event, None)
 return 'break'
 def _run_module_event(self, event):
 """Run the module after setting up the environment.
I'm getting more and more disappointed in the way Tk on OSX is moving forward.