I've tried various configurations but nothing seems to get multiple header images to rotate. Has anyone had luck with this?

Yes it works quite nicely.
Now, What version of Aahualpa and WP?
What is your url?
did you read http://forum.bytesforall.com/showthread.php?t=321

3.6.7/WP is 2.8/url: blog.wsd.net/mwooden

When I stated "won't rotate" I meant without refreshing the page.

works for me, I see the images fading in and out. you are on an old version of WP that HAS several security holes and you should upgrade it.

Hmmm, well it worked once...

Your image #1 is a vastly different size than the other images, try removing it and see what happens.

The rotate does not work for me either.
Just updated to Atahualpa 3.7.6 and after restoring the pictures for the header directory, I have tried with E 9, Firefox 11 in both Windows and Linux, Chromium in both Linux and Windows.
Images are located correctly, as I can see them, and everytime I reload the page, a different (randomly as set) image appears, but the fade in/out does not occur and rotation never happens.

What is the URL?
go to ato->export/import settings - export your settings and attach them to a reply (use the paper clip icon)
try disabling all your plugins to see if there is a conflict