I have built these two sites using your framework, www.loring-greenough.org and www.aftma.net. I love the framework. It's great. The setting for each of these sites for header is exactly the same except that with the aftma.net site they only show up on the home page:
The images at loring-greenough.org are not fading in and out but do change when clicking a different page or post category.
I will add that I have tested them side by side in the same browsers - same results each time.
How do I get them to fade in and out.