This bug dates back to at least Fallout 3 v1.7, I have never played an earlier version of that game so don't know if this bug was originally in Fallout 3 or later introduced through a patch. Anyways the bug is that if the FalloutPrefs.ini file does not exist, the Launcher application will generate a copy containing both the information from Fallout.ini as well as the information the Launcher application generates/configures. If FalloutPrefs.ini exists but the contents are deleted (A blank, empty file) then it will only add the information that the Launcher application generates/configures to FalloutPrefs.ini.

I believe the latter behavior is intended and not the former as duplicating various settings across 2 files seems really silly.