I've added a new widget area above the logo, but I can't get it to display in the Appearance > Widgets at all. I've deactivated a caching plugin, and refreshed dozens of times, tried it in other browsers and still no luck.

Here is what the code looks like from the ATO > Style & Edit Header Area text box:

<?php bfa_widget_area('name=header widget'); ?> %logo %pages %image

The URL is www.reapfoundation.org. I am using the latest versions of both WP and Atahualpa.

What am I doing wrong?

What version of Atahualpa?
go to ato->export/import settings - export your settings and attach them to a reply

I am using the latest version, 3.7.3.

The settings file is attached.

Using your settings, I'm getting a Header Widget area.

It finally showed up for me now as well, some 2 hours or more later. I'm having an interesting caching issue with this site for some reason. Thanks for the help!