I can't figure out why some of links appear normal (the sidebar widgets) while the top of page notice has links but they don't show up. I can see "inline" links that over riding my custom css I put in the atahualpa options. I even put !important to try to force the links to appear.

I am viewing through Firefox.

Also, on the right sidebar is a notice to guests. There are links in it but the viewer can't tell and no one is going to go to a site and hover over everything to see if there are links.

Any ideas?

The site is http://cityhomestead.net

What do you mean by '...the top of page notice ...' just what is the top of the page notice?

debugging 101 - turn off all plugins and see if the issue still exists. if so, add plugins in a bit at a time till the problem returns and you will know the conflict.

Please point to exact links that are giving you issues.