I have been searching through the Forum for the answer and have found references to threads that mention this problem, but haven't found the actual solution. The site is www.tampapreservation.com and am using Atahualpa 3.5.3 on WP 3.0 (which is quite wonderful I must say for someone like me who is in way over her head when it comes to web design and doing this on a volunteer basis for a non-profit).
I had the Search box and standard RSS logos turned off, then turned them back on, and now they are off to the right of the page. It did this before I added the logo image and turned the blog title and tagline on, so I don't think it has to do with the size of the image or text. I am assuming this is something simple, but I don't know where to look to fix it. Thanks in advance for your help.