That bug report is talking about gtk and modifiers affecting bindings
(in the first comments at least), or maybe it even talks about your
problem but it is so long that I would ask to include the relevant parts
here.

Nevertheless, after reading your comments I came to the conclusion that
doing what you want is very unlikely to happen. To bind something in Tk
you have to a specify a string like "<Control-x>", but to do what you
want, it would have to change to:

import Tkinter

def test(event):
    if event.keysym_num == ord('x') and event.state & 4:
        print "Ctrl-x!"

root = Tkinter.Tk()
root.bind('<KeyPress>', test)
root.mainloop()

Maybe you can test this and verify if it works like you wanted. But I
really don't see IDLE changing to work like that.