Just in case anyone comes along later with a similar issue, I’ll share that I figured out how I got into this mess:
To create new sites in the network, I had been using BackupBuddy to export a template site, complete with some base themes, content I wanted all new users to see, and some settings that are the same on all network sites. This was a huge time-saver. And, it worked just fine for more almost 40 sites, up until WP 3.5 and the shift to “uploads/sites”.
Starting after I upgraded to 3.5, those cloned sites have very funky upload issues. Some have no upload_path at all, some have an upload-path with the wrong option_id, some use wp-content/uploads (shared with the main site), some were uploading the same file to multiple directories (for example, “uploads/2013/09” AND “blogs.dir/60/files/2013/09”).
I tested with creating new site through the network admin panel. No issues. Created a new BUB clone: more issues.
I’ve reported the issue to iThemes. They show multisite support for BUB as beta, and have hinted that they will not continue to develop it, so I’m not sure if it will get fixed or not.
BTW, it wasn’t until I started to sort this out that I realized that when WP uploads, it creates the date directories based on the original publication date of the post/page. THAT finally explains why a cloned site I created last month has upload directories for 2012!