I guess you've modified the original game's LUA-files?
If you start a FaF-game, a separate LUA is loaded, so you need to modify the settings in this file. But if you modify it, everytime you start a new online game they won't match with the other players and cause a desync (or it automatically downloads an unmodified version).
The easiest way if you only want to use it offline (against AI's) is:
- copy init_faf.lua to init-faf-custom.lua in 'c:\programdata\faforever\bin\'
- edit the copy with your desired changes
- start FA with a modified shortcut: 'C:\ProgramData\FAForever\bin\ForgedAlliance.exe /init init_faf-custom.lua'
Should work