UPDATE: Atahualpa 3.6.7 with working custom widget areas, everything up to post #7 taken care of
Download Atahualpa 3.6.7 here
Because the requirements for themes listed at wordpress.org have been restricted, the ability to add custom PHP code through the Atahualpa Theme Options had to be removed.
If you have custom PHP code somewhere in the theme options the code will be printed now instead of being executed (Edit: Except for <?php bfa_widget_area('....'); ?> which will be executed. ).
The theme options "Content above LOOP", "Loop", "Content below LOOP", "Content if NOT FOUND" are gone now, to edit the Loop or to add code before/after the loop, you'd have to manually edit Atahualpa's index.php now.
3.6.6 also contains all of Juggledad's 364-XX bugfixes
3.6.6 has been successfully checked with WP_DEBUG TRUE, and with the Theme Check plugin.
EDIT: As pointed out by Juggledad, existing custom widget areas will not work in 3.6.6 because they ARE dynamic PHP, at least if you add their code (<?php bfa_widget_area(...); ?>) through one of the Atahualpa Theme Option text areas.
3.6.7 with a fix for custom widget areas is coming later today. If you don't have any custom widget areas, 3.6.6 should work for you.