(See http://forum.bytesforall.com/showthread.php?t=11814 for details on getting the rotating header to recognize images in Dashboard > Media on WP Multisite.)
The regex used in functions/bfa_rotating_header_images.php doesn't work for images that have been uploaded through Dashboard > Media. WP adds an image dimension to the filename, which Atahualpa is not looking for (eg atahualpa_header_2-1024x100.png). The following modification to the regex worked for me:
$files = m_find_in_dir(get_option('upload_path'), 'atahualpa_header_[0-9]+(\-[0-9]+x[0-9]+)?\.(jpe?g|png|gif|bmp)$');