So, I have one of those potentially dumb questions, and I feel like sharing it with everyone, to see what I can learn from you. Here comes the rambling extrapolation.
I was busy at work, when I had some stray thought about people who want to build real AIs, and my usual quandary: "why would you want to build a machine that can say 'no'? If it can be so hard to get people to actually work (we can be very lazy, and unmotivated), what makes you think that the machines will?" We've all seen Terminator's Skynet, and various other machines that, upon becoming self-aware, eventually look at their soft, squishy masters, who need them for so much, with all of our wastefullness, except when we maintain things out of guilt, or some "artistic aesthetic", and say "why not just get rid of them?", and yet still people want to build sentient machines, presumably for even less necessary human oversight, only strengthening the idea that we aren't really important. I then had this thought about something like that in 40k. I imagined some Tech-Priest, total heretech, of course, trying to recreate the Men of Iron, or some other "abominable intelligence", and when a group confronts him, he explains that he is doing it to help Humanity evolve. Evolution is only achieved through adversity, and while everything in the 40k galaxy does seem to want to indiscriminately kill (other) humans, our mastery of our surroundings, environment, and such has left us in a spot where we probably won't evolve again; we'll either become stagnant, and decadent, or disappear so fast evolution never had a chance. To remedy this, said crazy Tech-Priest sought to put that one thing Mankind has that matters, his mind, into a body far superior to ours (every Tech-Priest knows it is; that's why the tech up), and let that ever-changeable body, and others like it, take the next step in Humanity everywhere. It will wipe out this Humanity, but that was corrupt, incompetent, and such, and needed to be purged. What would happen would then be up to the players.
Now, for the seemingly loosely-related actual question: How does Chaos corrupt SOME machines? One theory states that the Men of Iron were corrupted, maybe even possessed, by Chaos, and this is what caused them to go rogue, as opposed to the usual "Humanity is unnecessary" schpeel AIs often develop; then they were destroyed. One of the reasons Servitors are so "primitive", much of the time, is to prevent them from being corrupted, and even ship cogitators, without a scrap of human flesh, or a soul, within it can be corrupted, and possessed by daemons. So, what protects our good friends the Newcrons? The C'Tan are mighty, but I've never seen the fluff try to claim that their paltry power can compare to one of the Ruinous Powers, whose very essence can harm the Star Gods (I don't even think they are often portrayed as as powerful as the various Greater Daemons, in table top), so if Chaos can corrupt the servitors and cogitators of Humanity, possibly even the most advanced machines we ever made, why can't they possess the Necrons? Lots of these examples "have no soul", but that doesn't stop Chaos from damning them, and taking over. Anyone know what the deal might be?