I checked two of my sites which use ATA and both have only 935 lines of code in the functions.php file. Don't know why info would be missing. I believe I removed the ATA and wordpress line from the footer on one but that would have been the only change...

What version of Atahualpa?

Both sites are 3.6.1

well you did say http://sweetboutiquellc.com was at 3.6.7 and I'm always looking at the latest code.

Yes that is the code for 3.6.1 and it should work. You can check by looking at the source of the page and checking which version it is using: the 1.4 or 1.6 version

Yes, that was one of my sites, but thought I'd test it on a less active one. Sorry about that.

I added the code, and it fixed the problem for Firefox. But still having the white flash on the other browsers. Do you know if I need to add the code in multiple places? Or perhaps it's a bit different for the other browsers?

Juggledad's development 101 - lesson 1

when making changes to a site, make sure all caching plugging are deactivated and the caches flushed so you can see the changes right away. Once the site is as you want it, you can turn them back on

Thanks for the advice! However, for this particular site, I have no caching plugins installed. I did clear the cache of each individual browser, but that didn't seem to help...

which site, the two 3.6.1 sites showed w3total cache in the source
muzzproduction and muzzmarketing

I tested on laubertool.com since that is the least active site I have.

I thought you said that is the site that it stays steady?

I do have one other site where the header remains steady during reloads.

http://laubertool.com
single header image
wp version: 3.0.4
ata version: 3.6.1
theme header options:

Prior to my upgrading to the latest version of WP, yes it was steady.

Well that site is getting the 1.4 version so I think you are in the same boat as everyone else and will have to hope WP fixes this

I have posted to the forum but no response. Do you know of a better way to reach out to Wordpress?

you might want to look at their bug reporting system, see if there had posted about it

Not so much a solution as a workaround to at least make the white flash less annoying.
1. I found this suggestion here:

In your style.css, create an entry for HTML.
Like this -

HTML {
background-color:#000;
background-image: url(images/background.jpg);
}

2. I tried several places within the Atahualpa file structure and finally found that if I took a portion of his suggestion (just the color) and put it in css.php, just before:

body {
	text-align: center;  /*

I now get a flash that is the same color as the background on my toolbar, so it, while not fixing the problem, makes it less annoying; at least to me.
The actual snippet I put there was:

HTML {
background-color:#1D242B;
}

Hope it helps...