It’s very possible with your height you were way over the necessary jacking to get the kart to turn on your old setting, and taking all that geometry out helped settle the kart down and actually made it usable.
That’s why I always try to shy away from generalizing anything in kart setup because as you’ve just demonstrated, depending on the conditions, you may end up with the opposite results of what is expected.
Karts work within a “box” with regards to setup. There’s a window where the kart reacts predictably to changes, on some chassis this window is bigger. Things like driver size, tires, engine, weight can all alter the size and placement of where this imaginary “tuning window” is. Once you get outside that window, the kart might not react as you would guess because you’ve over-stepped a line somewhere on your setup and the kart is operating outside of it’s comfort zone.