This morning I discovered that the Atahualpa theme option menu had stopped working on a number of WP installations, with all menu options returning to the initial landing page.

I worked out that this was only happening on those sites on which I'd installed the MP6 (admin UI hack / re-styling) plugin, which had recently upgraded to version 2.0. Deactivating MP6 (which is mainly cosmetic anyhow) solved the problem and restored full admin functionality.

Just a quick heads-up in case anyone else is experiencing a similar issue with the Atahualpa admin menu.

Why in heck are you even using it? From the plugin page

This is a plugin to break the wp-admin UI, and is not recommended for non-savvy users.

It's an experimental UI enhancement, which I preferred to the standard WP options.

And I think the Plugin authors probably intended that statement ironically