Here's the smallest example I could come up with for a rendering problem 
i don't know how to debug:

using tmp.org=

    * asd ** def

and tmp.el=

    (require 'package) (add-to-list 'package-archives '("melpa" .
    "https://melpa.org/packages/")) (package-initialize) (setq
    package-enable-at-startup nil) (setq org-ellipsis "…") (find-file
    "tmp.org")

then starting from the shell:

    emacs -Q --debug-init --load tmp.el tmp.org tmp.el

i get a nicely split frame with an org buffer that has an underlined 
ellipsis.
removing package-initialize from tmp.el and starting again fixes this.
am wondering how to debug or better define the issue.

m