Rory,
The navigation disappearing on the home page is caused the slider script. Like you said, it only happens in Chrome, and even more than that, Chrome on Windows. I filled out an issue request with the slider developer to see if they have any idea.
In my experiments, it only happened when I had a light navigation item with a dark background. When the navigation text was dark on a light background it was still visible. It’s rather odd, but at the moment I don’t have a fix for it. As soon as one is ready, I’ll publish an update.
I took a look at your site. Great job by the way. The text widgets at the bottom have some anchor tags that may be causing the IE layout troubles. There is a link that’s opened in the first text widget that isn’t closed until the second one. There is also a closing one in the third widget without an opening one. Try adjusting those and see if that doesn’t fix the IE trouble.
If I can help with anything else, please let me know,
Bill