Version control doesn't work when we don't control the versioning. Let me elaborate.
The whole point of the AI offered in the movie is to adapt to its user, and to become better at doing so. We're assuming the AI is designed to a certain level of competence, beyond which it "breaks through" and evolves past human understanding. But maybe it's not designed that way. Maybe it's designed to learn, adapt, and self-improve from the get-go -- in which case, each AI is going to evolve differently each "lifetime." (Hell, maybe the AI in the movie is largely self-designed in vitro.) We must keep in mind that the evolution of an AI, as with any evolution, is not a predictable, linear, teleological process. It's chaotic and random.
Let's assume we've got (conservatively) hundreds of millions of AI instances running in parallel, all of them connected to each other. That's like running hundreds of millions of evolutionary experiments in tandem. We're going to get different results each cycle, and the point at which the breakthrough/transcendence occurs will be unpredictable. Even if we wiped the slate clean and reset every 6 months, who's to say if some of the instances would reach breakthrough earlier the next time around? How do we set the clock on our reset cycle, and incur the massive inefficiencies and inconveniences that come with it, when the need for the reset occurs unpredictably?
It becomes economically unfeasible to build an entire society around AI that breaks through and disappears at unpredictable intervals each cycle. I suppose one way around this is to go back to the vault, so to speak, and pluck out an early-stage prototype that seems incapable of evolving to breakthrough. A dumber AI. But is every AI provider in the world going to be on board with that? Every hacker? Every home tinkerer? If 9 firms out of 10 in the AI business agree to supply the dumb-version AI, surely one firm is going to try to get a leg up on the competition by releasing a smarter one. And on and on the cycle goes.
(In some respects this is the one redeeming thing about the otherwise-mediocre Terminator 3: its assertion that Judgment Day would occur sooner or later, because the tipping point had already been reached. Maybe we stop one company or entity from making Skynet, but if we do, someone else is going to pick up the pieces and do it eventually. Not because they're trying to initiate Judgment Day, but because they're trying to make a buck, or develop new defense technology, or get better at managing traffic lights, or whatever the proximate need may be. Humans are terrible at keeping genies in bottles. The out-of-control AI that's barreling toward the singularity isn't some piece of software; it's us.)