Hi Mark,

After removing the patch to ob-python.el and applying the attached patch
to python.el, could you please test that your notebooks work again?

This will probably not change the independent initialization problem
that you describe (but it might, who knows).  If you want to help me
understanding that part, you can do

  M-x trace-function RET python-shell-send-string-no-output
  M-x trace-function RET python-shell-output-filter-buffer
  M-x trace-function RET python-shell-completion-native-get-completions

and send the result printed to 'trace-buffer'.  Thanks!