I was having this issue on page load/page switch. The pages displayed in full for a ms before doing the fade-in site wide animation.
This is what I used to fix it (add to custom css section in settings)
body:not([data-animation-state="booted"]) > * {
opacity: 0;
}
This waits for the 'data-animation-state' attribute to be added to body before showing any elements, essentially skipping the full display that happens before the animations are queued
Hope this helps!