It should be noted that all of the below is working from memory, as I am away from my books.
Away from my books at the moment, but I believe the "problem" with nanites started with the Sybil/CFD Virus. Basically, AI's and E-ghosts have figured out some way to copy themselves into a biological body; nanites tend to be their most effective carriers. It should be noted that nanites are not required to have CFD, but they help facilitate the infection and control process.
Usually, the process of CFD taking over a host completely erases their personality and will. Sometimes, a person will resist, in which case you get headcases. Headcases are usually not the picture of sanity, as they go between multiple personalities (their own, and whatever he CFD virus fragments into; I think I remember an NPC who once had 5 personalities); although FastJack actually could be considered a headcase, as he is stuck with the AI S.E.A.R.C.H. (Forget what the acronym is for, but I believe it used to be a military combat program) in his head.
CFD is not limited to biological forms. Since it uses nanites as its carriers, it can infect anything that uses nanites to construct and maintain. I know the AK-147 line, which was entirely nanofaxed, has become obsolete, and I'm sure other things have happened as well. I don't think it's been a world-wide problem, because almost everything uses nanomanufacturing (from clothes, to guns, to cyberware, to a bajillion other things, they all use nanites) in 2075. That's the easiest way to mass-produce and make a profit on stuff. Still, it could be a problem.
Anyway, been on a plane all day, I'll check back in on the IC and probably make a post; sorry for my inactivity most of the day.