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