Ok, I am nearing the end of the game. lvl 26 and almost ready to head off to the final battle... Legion and NCR both accepted me... Though for some fun I'd go slaughter every single NCR base... Got them to villified... Then proceeded to go and kill Caesar with my bare hands, up to which point I had reached villified status as well... Then after leaving the fort I checked... NCR and Legion were no longer on my reputation stats and all the outposts of NCR and Legion are considered "neutral" Is this because I annhilated them or is something wrong?

If you're wearing any Faction armor, it all comes up neutral.