I have seen this twice now and have heard talk of it on the PC forums so I think for sure its a bug. There is no way to return from a Vilified rating with any faction EVEN if you actually do so, that faction will always attack. There are two cases in which I have seen it as evidence.

1) Vilified the Pwder Gang at beginning, then reduced them to Merciful Thug at Vault 19, they still attack at NCR Prison even though it clearly says Merciful Thug on the map.
2) Vilified the Caesars at Nelson, then went to the Strip and recieved Mark of Caesar and was made neutral again, however all Caesars attack on site still.

PC players say that when they try to change reputation using console it doesnt seem to work from vilified.

ANybody else seen this?

This is happening to me on the xbox. I cant get into Caesars tent to speak with him becasue they attack before I get close.

Are you sure you're not wearing faction armor? If you're wearing NCR armor then the Powder Gangers and Caesar's Legion will attack you no matter what you do. You have to change into different armor in order to not be attacked by them. Also, some Powder Gangers will attack you no matter what, but if it's the one's at the NCR Prison, then you're probably wearing NCR armor or something.

I'm not actually sure if factions are supposed to outright attack you just because you're vilified. I've been vilified with the NCR for quite some time, and they let me into the South Western checkpoint base with the huge monument at the front all the time. The only thing is that I get Ranger hit squads after me every now and then.