I have a similar problem. None of the mentioned solutions above have helped me.
I noticed that ScrollTrigger calculates wrong as long as the current container is in the DOM structure AND if the current container is higher than the next container, even though I positioned the current container absolute/fixed while transitioning. Only when using ScrollTrigger.refresh() in the "after" function, ScrollTrigger calculates correctly, but that is not helpful because users can see elements "jumping" to the correct position.
So I decided to remove the current container in the "beforeEnter" function, then trigger ScrollTrigger.refresh(), also in the "beforeEnter" function, since I do not need the current container after removing.
Note: I'm also using Smooth Scrollbar, so there is probably some conflict there, too.
