I have a fixed header that appears at the top of my website, and stays on top as you scroll down, except that it disappears over the hero unit area.
Any advice would be appreciated.
Here is the site - http://fromgreatchaos.blogspot.com/
You should try to post the relevant pieces of code here along with your question, to make it easier for people to answer.
I just took a quick look at your site, and it seems like you're using a variable called aboveHeight
that controls when the header is given "fixed" (hovering) positioning. That variable is being set to the height of the "hero" element, so the "fixed" position of the header only applies after the page has been scrolled past the height of the "hero" element.