(Sigh) They were are in /uploads/.
But here's the really weird thing:
So the whole issue came to light when after an update (I'm thinking 3.6.1), some sites in the network were missing image headers, then I discovered some sites were missing other images too. At first, I thought it was an iThemes' Builder issue, but then two non-Builder themed sites were affected.
So this afternoon, after thinking that it's an upload path issue, I started trying to tracking down the missing image files in backups. The missing images were still listed in the affected site media library, and in the media library, individual file urls showed that the file in blogs.dir/#/files, but weren't there!
I found these files all in /uploads/. They have been there in all my oldest backups. Out of curiosity, I copied the files into the correct blogs.dir folder, and voila-- all the images on the site were back!
Up until Aug 4 (I'm thinking that's when I updated to 3.6), all the media files in /uploads/ were only for the main site. After that, there are files for a number of other sites mixed in there. For instance, the image header for one site shows it's URL in the media library as: http://subsite.mainsite.com/wp-content/blogs.dir/66/files/2013/07/imageheader.jpg, BUT that file is actually located now at wp-content/uploads/2013/08.
But I KNOW that this site was functioning normally and displaying this image header correctly about 10 days ago. When I copy the image file to the blogs.dir location, the issue is resolved.
So I'm thinking that the uploads issue from the 3.6 update might have started this. Here is my original post: http://wordpress.org/support/topic/media-files-not-uploading-to-correct-dir-after-wp36?replies=10
What I can't figure out is why the update to 3.6.1 triggered this all over again!
I will get all the images in /uploads/ that don't belong there moved back to their folders, and check the uploads path for the affected sites to double check. [But I also know I have at least one subsite without an option for setting "uploads path". Not sure what to do about that one!]
What I can't figure out is why those image files from Aug 4 onward that were in /uploads/ (they appear there in all my backups), with file urls to blogs.dir, suddenly stopped working with a WP update.
Think if the files keep going to /uploads/ that they will keep having this issue every WP update?
And making sure the upload path is blogs.dir/#/ should keep them from going to /uploads/, right?