Without looking closely at it, I would speculate that the failures are due to trying to test code in overrideRootMenu() that was previously only called once during execution and may not be re-enterant:

    # Remove the last 3 items of the file menu: a separator, close window and
    # quit. Close window will be reinserted just above the save item, where
    # it should be according to the HIG. Quit is in the application menu.
    del mainmenu.menudefs[0][1][-3:]
    mainmenu.menudefs[0][1].insert(6, closeItem)