I assume a lot of people have this problem, so I do hope that some one here can help me with it. I have searched google but can't find anything decent.

Apart from this bug I have no trouble at all with the game, I start the game as normal and I do not kill the group of Legionaries that is inside Nipton, I carry on as normal to the east where there are a bunch of vehicles and mines under some cones on the road, and where there are 4 raiders, 3 on the mountain and 1 just behind a rock. After dealing with them I always come across a Legion Patrol to which I utterly destroy.

Now my problem comes, after dealing with the patrol my status with the Legion is now Vilified. Good right? After all I want them to attack me on sight. But no it doesn't work like that, just after I meet the trade caravan that consists of two traders and some guards that you first meet on the bridge not that far from where the legion patrol was, I follow them as I know a group of 4 Legionaries are waiting to ambush them.
Sadly they are friendly with me even though I'm vilified, and all of the Legion are friendly with me in the entire game. I've done this process over 10 times hoping that each play through is different then the last but sadly I keep getting disappointed. So I figured I may as well start a new game and this time be friends with the legion and attack all NCR on sight. But guess what, the same [censored] problem arises.

So can any body help? And yes I have all the patches including the one that was supposed to fix it.

PC? What mods you using?

Otherwise the only thing I can think of is have you equipped faction armour for either one? It may have bugged in which case you need to re equip then unequip it. Other than that...don't know, haven't heard of it happening to two factions like that...

Right I should of said so my mistake.

I have no mods at all, I don't really like them.
I do not wear faction Armour, I do not have the mark of Caesar or the NCR equivalent.

Well, grab a certain companion in Novac and he'll shoot them on eight which is pretty much the same effect

That doesn't fix the problem. Companions make the game to easy.

Have you tried taking on the legate with a companion..blade to the face of your companion hehe. Then what?

Can we not go off topic and concentrate on the problem at hand? Which is the bug with the factions.