I don't know exactly what triggered it but my fame with the NCR was completely taken away at some point when I was in caves at Guardian Outpost. I don't know if the speech check in the caves did it or what but the entry in the general tab completely disappeared. I travelled back to the NCR camps and they treat me indifferently now. So, to reiterate, my NCR entry was completely erased and removed form the General Tab in the Pipboy, only when I returned to an NCR outpost to turn in a quest did I get the entry back, except it was now neutral instead of liked.