Go into \Steam\SteamApps\common\fallout new vegas.
Make a backup copy of the Fallout_default.ini then add your tweaks there then delete the two .ini files in C:\Users\your name\Documents\My Games\FalloutNV and let it rebuild them.
Go into D:\Steam\userdata\your user number\22380\remote.
Make a backup copy of falloutprefs.ini then add your tweaks there, or as others suggested, delete all the files in that folder then make it read only.
I hate the cloud.