Does your init.el file include anything besides these two lines:

  (require 'org)
  (org-babel-tangle-file "~/.emacs.d/settings.org" "~/.emacs.d/settings.el")

Does the problem persist if you remove everything except those 2
lines? 

Does the init file get written the custom-set-faces for,m
which records the font and the size you selected?