Fixing the call to get_children() in gallery_shortcode() as rtz suggests should allow [gallery orderby="post_name ASC"] to sort the thumbnails by name, but the prev and next links will still be sorted in the default. That’s handled in adjacent_image_link() in media.php and I’m not familiar enough with the code yet to know if you can access the orderby shortcode option down there or if you have to just hard code your desired sort order until an official fix is released.
