With WP MultiSite, bfa_m_find_in_dir.php appears to create a header image array that includes every folder and file in blogs.dir/n/files/ for subsites, and in wp-content/uploads/ for the primary site.
This behavior is the same whether header images are placed directly in the files folder, or uploaded via Media Manager (according to the new instructions). It does this with a single header image file as well as multiple image files, rotated or not. (Yes, files that reference /wpmu-settings.php were changed to /wp-includes/ms-settings.php and I also tried using is_multisite(), with same results.)
With a single-site installation, version 3.7.6 works fine. I rolled back from 376 to 367 on multisite, except for a test web with no plugins. If you paste the 376 bfa_m_find_in_dir.php contents into the 367 version on a multisite that's working fine, you can also replicate the problem.
I've been using Atahualpa for several years and this is the first time I've had a serious problem, so I'm optimistic about a fix.