I find that, in order for the theme to read my header (while preserving the header from future updates), I have to do one of two things, seemingly contrary to instructions:

1. Simply put it in wp-content > ata-images, with relative image location set to wp-content > ata-images rather than to wp-content > ata-images > header; or

2. create a header folder (wp-content > ata-images > header), place the header in that header folder, and set my relative image location to wp-content > ata-images/header.

I've gone with option 1. After days of unsuccessful efforts to make my header visible, this works. Now to figure out why my favicon doesn't show ...

Without your URL it will be hard to help you determine what might be going on.

If you are using the atahualpa header with no plugins, and (as of 3.7.13) you
1) specify the 'Relative location of images?' as being 'wp-content' and
2) use 'ata-images' as the 'Images Directory'
the images will only be grabed from wp-content/ata-images/header. You can see this by looking at the source of your page.

If you specify
1) specify the 'Relative location of images?' as being 'atahualpa'
the header images will come from the 'wp-content/atahualpa/images/header' folder

The only way it could come from somewhere else is if you modified the theme code.

URL: http://k12photoed.org

Here's another site I publish where I have the header installed (and read correctly for display) in wp-content > ata-images > header: http://teachingphoto.com

Not sure what's different between these two, but I haven't altered the theme at either.

Not sure what you mean by "no plugins installed." I do have assorted plugins installed, but none related to my header. Pretty much the same plugins at both sites.

I can provide you with a login and pw if that will help.

Looking at the source code of my site, I find the following:

<table id="logoarea" cellpadding="0" cellspacing="0" border="0" width="100%"><tr><td valign="middle" class="logoarea-logo"><a href="http://www.k12photoed.org/"><img class="logo" src="http://www.k12photoed.org/wp-content/ata-images/headerneweyes.jpg"

Verifying this in Dreamweaver, I note that my header -- headerneweyes.jpg -- resides in wp-content > ata-images (and not in wp-content > ata-images > header). And gets read correctly by Safari, Firefox, and Chrome.

In ATO, I verify that my settings are: Relative location > wp-content, and Images Directory >ata-images

So I have trouble reconciling this with your assertion that

If you are using the atahualpa header with no plugins, and (as of 3.7.13) you
1) specify the 'Relative location of images?' as being 'wp-content' and
2) use 'ata-images' as the 'Images Directory'
the images will only be grabed from wp-content/ata-images/header. You can see this by looking at the source of your page.

You might want to go read the onscreen documentation at ATO->Image Location->Image Locations. Then read the onscreen at ATO->Style & edit HEADER AREA->Style & edit HEADER AREA so you will understand the difference between a 'header image' and a 'logo'.

I understand (or think I do, and have so far) understood the difference between a header and a logo.

However, in the case of http://k12photoed.org, the only way I found to get the theme to make the header image visible online was to take it out of the wp-content > ata-images > header folder and put it in the wp-content > ata-images folder. So long as I had it in the wp-content > ata-images > header folder, it wouldn't display.

True also at http://teachingphoto.com

I understand that ATA may be reading my header as a logo in those cases. So long as it displays, I really don't care. I do know that if I move these two headers back into their respective wp-content > ata-images > header folders, they don't display.

In my several other ATA-themed blogs, the header image resides in the wp-content > ata-images > header folder, and displays properly. This is true at:

http://www.nearbycafe.com/loveandlust/eroticbynature/

http://www.nearbycafe.com/artandphoto/photocritic/

and

http://www.nearbycafe.com/artandphoto/liuxiaphotos/

I have no idea why this should be so. But it is. So far as I know, the settings for all these blogs are the same (aside from image location, etc.): headers in the the wp-content > ata-images > header folder, with settings to match.

I consider my primary concern the proper display of the headers at my sites. So long as they survive the ATA updates in their current location and settings (I just upgraded to 3.7.15), I don't really care whether I'm somehow fooling the theme into treating them as logos instead of headers with these two installations of WP/ATA.

I'll gladly send you logins/pws if you want to look under the hood at any of these sites.

Again, you should read the on screen documentation. If you want header images ( and you can have multiple header imager and make them rotate) you use %images. If you want a logo to display you use %logo.

Two separate things with different options for each.

I understand that ATA may be reading my header as a logo in those cases.

Atahualpa is reading your logo as a logo, you need to learn the terminology and read the documentation. As it stands the software is working the way it is intended to which doesn't seem to be the way you assume it should work.

P.S.

I understand (or think I do, and have so far) understood the difference between a header and a logo.

However, in the case of http://k12photoed.org, the only way I found to get the theme to make the header image visible ...

go look at ATO->Style & edit HEADER area->Configure Header Area and I think you will find you are using %logo and not %image...