Well, as I said there is not much you can do from a logical perspective. Currently for the nav to be highlighted something has to happen that would be reflected on the nav, right? So this something is an element’s edge crossing exactly vertical half of the screen. This makes nav to highlight the corresponding link for the crossing section (that is why small first sections will never be highlighted - they never cross the center of the screen).
How do you want it to work differently? So that the highlight happen when an element’s edge crosses some line at the top of the page? In this case sometimes you may end up with most of the text on the page being from the next section but a tiny bit of previous section will juuuust crawl through this upper line and your nav will tell you that you are on the previous section even if it is barely visible.