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:

rotate: 5
shuffle
fade: 1
preload: yes
clickable: no

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.

Try turning off the animated menu on the site that doesn't work. If that doesn't work maybe it's a plugin conflict issue.

This site was originally built using a cutline 3-split template where I had to install what was suckerfish (now pixopoint) to get the drop down menus to work but the php was added to the header.php of the cutline theme and should have been disabled when I moved to the new theme.

I have now deleted multi-level navigation and the cutline 3-split theme and it's still not rotating.

It looks like the Animate Page Menu Bar is still set to yes in ATO>Menu 1. Try setting that to off and see if the problem persists.

I turned off the animate option and it's still not rotating properly. Any other ideas for me?

Do you have ALL the 3.6.7 patches applied to the loring-greenough.org site? If you do have you tried deactivating all plugins to see if there is a conflict?

go to ago->export/import settings - export your settings and attach them to a reply (paper clip icon) and I'll test them.