It might be messing with the oblivion.ini file, which is used both for Nehrim and Oblivion. it contains a section called "fonts". You should check if there were any alterations.
Id probably recommend one .ini file for Nehrim, and one .ini for Oblivion, if you use a MOD to change the font, or maybe make the .ini file read-only, so it cannot be changed.
But there might be another cause for this as well, thats the only clue i got.