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Michiel de Hoon's comments re this Bug on python-dev:
http://mail.python.org/pipermail/python-dev/2005-January/050895.html

In IDLE there are two processes.  One runs the GUI and
communicates with the second via the socket interface.  The
subprocess has two threads: MainThread, which runs the user
code, and SocketThread, which monitors the socket interface.
SocketThread communicates with MainThread via two Queue
objects and several global flags which are involved in shutting
down the subprocess.

So it's the subprocess (run.py) MainThread that should call
PyOS_InputHook.

See Patch  989712.  Noam Raphael is trying to hook in
tkinter's mainloop.  This should all be solved together.

Putting it back in IDLE for now so I can keep an eye on it.