This started happen to me since yesterday, I can freely walk (well almost... Sha Enin is a bit mad on me, but he's usually dead, so it's not a problem) at bazaar, but if I go inside inner city they will shoot me instantly without warning, even if I have no item in main hand, the problem is I have like -2k rep with Free Traders, but it shouldn't be the case, because blue cops starting shoot 1st at me (and I don't think they're traders), and only after that every guard shoot. Also I don't lose -100 rep with NCR after that, so it's not my fault, they simply.. don't like me ;p
Edit: Ah and yes, I hope devs will repair reputation losing over time, because it's possible to to get atleast 651 (or 650, don't know exactly) reputation with NCR by trading (yes, if traders are alive) and then join BoS, you'll have 1501 reputation with NCR. It means you're Idolized and guards don't care about anyone who you shoot, only if your victim has atleast 901 (or 900) reputation.
You'll lose like ~ -10 reputation every 2-3 real life hours being offline.
If you're online 24/7 (afk on World Map when not playing) your reputation won't change at all, so you'll be perma-Idolized and may kill anyone at NCR for fun.