What a job you've got processing all these queries!
I think this thread is something like the problem I'm having with Ata navigation and multiple post categories.
When a post has multiple categories, the bfa_navigation code chooses the 'default' category (with the lowest ID). Choosing any other category from the site menubar (other than the default) means that the navigation does not show the other posts in that category.
I'm using the latest version of everything, and have tried "sCategory Permalink" to change the default category, but to no avail. Is there any modification I can make to Atahualpa ?