Just get rid of the damn headers. Users don't want them. They are just misguided ways of trying to raise retention, but really what they do is make your site less pleasant to use, which then makes me not want to come back later.
I absolutely loathe fixed headers, but I think this script is pretty cool. The headers stay out of your way when you are reading, and when you actually want to use the navigation you don't have to scroll all the way to the top. I really see no downside, except "more JavaScript." (People who are complaining about JavaScript: you really aren't going to like the Web in 5 years)
Downside: unusual behaviour. Users fully understand how to scroll to the top of a page to find the header. This hack already requires them to scroll up to get to the header. Also, there's a decent chance that if you're trying to find the header that you're going to leave the page, so it doesn't matter if you lose your spot.
It's a cutesy feature, but it's cumbersome and pointless, and doesn't add any real usability (unless you count getting rid of fixed headers, which also don't add any real usability).