It says she's getting payment for the terminator movies as well, and all three matrix movies. I wonder...why didn't she sue after T2 did so well? And why would Time-Warner continue making the other two movies along the same lines, after a suit was filed in 99?

It's possible that they thought they were changing it sufficiently to be their own creation, so they went ahead. Maybe they thing they're in the right, genuinely. We'd have to read Stewart's works to be sure. It's possible it's true, but there's many things that don't make sense in there.