I recently automatically upgraded the Atahualpa theme (before reading that was the wrong way to do it) for my site, http://nyc.sierraclub.org. I was able to update the header image and the Site title is showing correctly in the logo space. However, I cannot fix the logo icon. I've used logo.jpg, .png, and .gif. I have put this in every image field I can find, but it's still not showing up.

I didn't have this problem when I originally put the site online, so I can't figure out what is wrong. Thoughts?

You mean the green tree in the circle? I see it fine in Safari