Search box, tags and categories no longer link to posts

Greetings!

I recently updated to WP 2.8.4 (successful) and shortly thereafter updated to Atahualpa 3.4.1. My blog posts and general appearance came through just fine, although I did have to reset link colors. I have not, however, been able to get the tag cloud, categories and search box to link properly. If I click on a tag or category they come up empty. Likewise, if I enter something in the search box, it also comes up empty. Both tags and categories are still there. If I go to Post Tags from the Dashboard, for example, all my tags show up and, from there, will "attach" to the appropriate posts. They just won't work from blog page.

I've searched the forums but have not found a solution. I've removed and re-added the tag cloud and categories to no avail. I'd greatly appreciate any suggestions for resolving this.