I was having this issue with the big text described in the above images as well using Mod Organizer. I found that editing both fallout.ini files manually did not fix the issue. Instead in the mod organizers tool bar (puzzle piece one) edit the fallout.ini through that and save. I found that editing the ini this way was strange since i did it manually, something must overwrite something in the injection process. Anyway i hope this helps someone in the future.