> then I can try to investigate what could be causing the Emacs org
> to load. I cannot see how that is possible since it is not even
> available on the elisp path anymore.
>
> Is there a way to check which elisp files have been loaded? Then I can
> grep for anything from the emacs org install instead of my local
> install.

`locate-library' may help. Also, `load-path' can give a clue. Try with
a bare configuration, i.e., with just

  (require 'package)
  (package-initialize)

It can be tricky to find out what is loading bundled Org too early.
Enjoy the Frankenorg.