I am wondering if I am missing an easy fix. Ever since that last patch every now and then it replaces my fallout ini font changes. I am using fallout mod manager to launch the game, so it shouldn't be doing it

Does the default launcher go up? If so, it switches the INI to the info from a file in your main Fallout directory, called "Fallout_default" or something along those lines. Your solution would be to edit that file so it replaces the INI with what you want.