I then follow the marker of the main quest east along a road where there are abandoned cars, mines under cones and vipers I think upon the mounts waiting to Ambush you. After killing them I carry along the road north and there is always a Legion Patrol that consists of 4 men and some times 2 dogs. As I'm neutral at this point they do not attack me so I attack them and take their gear but I DO NOT equip it. I either get Shunned or hated at this point but never Vilified. I then head into the Cabin just up the hill on the right of the road where the unique Cleaver is. I rest for an hour and carry on towards the Bridge that 2 Travelling Merchants are passing. Sell the stuff I picked up from the dead Legion members and go along the road where there are two groups of two Legionnaires on either side of the road, one group infront of a bill board and the other just on the right but a bit hard to see. Seeing as I'm either Shunned or Hated they should be red at this point and attack me, but they do not so I kill them thus getting Vilified finally.
Now as I carry on long the road, just before the billboard where some vipers are hiding behind, the two Legion Assassins come after me. Some times they get into a fight with the NCR patrol in the area or they fight with the Merchants. Or rarely they meet both groups and get killed. But either way they die. Still Vilified and I understand they do not turn red until they speak to you.
I go towards the camp for the quest Booted where the two Powder Gangers are, but sadly the entire camp are blue to me. What ever, I kill them and do the quest. Now on every play through I quickly go to the Coves where you take a boat to the Fort and the entire place is blue to me. Same as Nelson. Yet I am still vilified. Its pathetic its gone on this long.
Same goes for NCR, when I kill one I see they are still blue to me and can still pick up quests. Its broken for me, but the chances that its like that after a patch and on both xbox and pc? And not only me have the problem.
It's interesting how games vary, in four or five playthroughs I've never encountered a Legion patrol up the road from the Viper ambush but the behaviour of the Legionnaires by the billboard is a variant of what I meant, they're part of a scripted event and that's why they ignore you.
Spoiler They're there to ambush the caravan. They usually lose but whoever wins you get a lot of loot.
I always get attacked by the Legion assassins just north of that point if I'm vilified too. I've never done the Booted quest but it, like the Cove, is a quest location and they don't always reflect the reputation you have generally. An obvious example of this is the Vipers who attack on sight everywhere except inside Vault 3 where they respond to your choices.
There is a reputation bug (randomly resets non-vilified reputations to neutral) but I don't think it's what your describing, which sounds more like the general illogicality of much of the game.