My site template used WP to generate the meta tags in the header of each page, but only my main page actually uses the WP functionality for blogging.
Any subdirectory that then tried to load resulted in a 404, though the page was actually returned correctly (Firefox displayed, IE displayed it's 404 until pretty error messages were turned off).
It appears someone added hard links in the WP code that don't refer from the proper base. Since WP has the base link already reference, I see this as a WP bug since I am not actually using the rest of the blogging functionality.
I've hacked this to only use WP on the main page, but I don't feel I should have to do this... Any comments?