I did search and I found that there was some people that had the same problem that I had and I was able to fix it.
My problem was the Fake_Fullscreen.exe was causing the FalloutPref.ini to increase in size. I discovered today that it was 42mb in size and that is when I started to reach out and see what the solution might be.
I took a base FalloutPref.ini and copied it over the bloated one. [which was full of duplicate entries] Tested the NVSE and the FNV4GB.exe and they did not increase the size of the FalloutPref.ini. When I ran Fake_Fullscreen.exe, the immediately grew in size.