[Theme: Atahualpa} Categories Menu Shows Only One Out of Many

Problem shows up when running the Atahualpa theme ever since we upgraded WP, Atahualpa, and our plugins a couple of weeks ago.

Now, all Categories menus when clicked only display one entry out of dozens of entries.

We turned off all plugins and it still is broken. We’ve triple checked everything.

I don’t see any other people writing on forums about this problem. Any ideas?