Having a problem with widgets

I'm using WP 3.0.4
I was using Atahualpa 3.4.9
I started having problems with Widgets: when I deleted them, or dragged them off the right sidebar, nothing changed; they stayed there. Plus, the affiliate code ID was altered between what I put in the code window versus viewing in the browser and mousing over the link, the aff ID was changed mysteriously. So, I decided to try to upgrade Atahualpa and went to 3.6.1and now, none of the settings in the style and edit header area don't respond. I can no longer get my blog title and tagline to display over my header image. There are so many versions of this, I don't know which to use. I really love your theme, but now it seems frought with problems. Any way to fix 3.6.1 so it responds to settings? Thanks so much.