Judging by the replies and my testing, I'm pretty sure you're right. You make an interesting point, I wonder what Perk it could possibly be. I might come back and post all of mine later.
I have a similar problem, and I think its simply bugged...
I am vilified by Powder Gangers and Legion. Powder Gangers should hunt you, I read somewhere. Well they attack me, when I meet one randomly spawned guy, but thats it.
I freed the hostages from Nipton, and killed several Legion, i am vilified since then, but they ignore me completely, except when I shoot at them. But immediately after freeing the hostages, and immediately after the games message that my status with the legion is now 'vilified' a legion killer squad teleported in, there was a message that Caesar has ordered my death, and I had to fight them. Since then - nothing. (My main quest line is only completed up to Novac, btw.)
What does not work, intentional or not, are random events. The game seems to have none, or very few. I can walk over empty desert for hours, with nothing happening. Is this normal?? There are very few monsters after you fight your way through for the first time, nothing to find, no small locations, no small stories (finding an note, or some...), nothing at all. And no random events I found.
The attacks of Black Talon in FO3 where an element of insecurity, added greatly to the game, and last but not least where a source of valuable items. I used their combat armor to repair mine for a long time. Now I am level 14, and have just leather armor. (I could probably buy better, but without finding more of this type to repair and maintain it, I cannot afford it). There was a better armor with a Jackal or Viper someplace before Nipton, but since then the location is empty, no respawn, did not find the armor everywhere so I have only one suit with no chance to repair (repair=50 for me) and Icannot use it since its badly broken as usual. Vipers and Jackals seem not to respawn, and there are very few of them.
I absolutely love it, that several monsters are dangerous for my character, I love the changes to weapons and ammunition - but resources are sadly lacking, there is not much to explore (fought my way past golden geckos in a radiated environment, which costs resources - only to find absolutely nothing. Is this normal??)
And I miss random events. No wastelanders fleeing, no Raiders, and no respawn (there are places in FO3 where always where some Raiders, in NV - nothing).
Is this a game bug, or intentional? The game now seems empty to me. Am I really forced to continue the main quest line to advance events? Why? I would love to do several side quests, but often I am lacking the resources for it. I fight a bunch of hard monsters (fine with me!) but afterward there is nothing to find, no reward besides the XP. Places are empty, the world feels small and empty, closed in and boring.
Pity. I hope this a bug which can be fixed later.