I was using WP 2.8.4 and Atahualpa 3.4.2 on a site, and just tried the Yet Another Related Posts plugin. It required building a new cache. Big no-no! Apparently that caused some weird problem. First, at the top of the page, instead of the header, I saw this: Parse error: syntax error, unexpected T_STRING in /usr/home/web/users/xxxxx/html/wp27/wp-content/themes/atahualpa342/functions/bfa_header_config.php(350) : eval()'d code on line 1
Thinking bfa_header_config was somehow corrupted, I installed a new copy of it. No difference. I tried another theme. I tried all 5 I had in the themes folder, including the default. They show no formatting, just plain-jane, with no header areas.
So this makes me think something in WP itself is corrupted. Short of reinstalling WP or doing a full database backup, can you think of anything to try?