In my experience (i’m not a pro) the problem are in the database fields and the wp-default fields … one set wp-content/uploads/sites/id/files/year/month (default) and the other to the old style (3.4-) wp-content/blogs.dir/id/files/year/month (data-base fields) … if you use a year-month set.
Why this, don’t know, is something that I’m trying to resolve too!
You can manually set this to the same linking wp-content/blogs.dir with wp-content/uploads/sites (if you know Unix-linux ln command).
You’re fine! Don’t do anything!
Why did this happen? Because WordPress changed 🙂
wp-content/uploads/sites/7/ – This Multisite was created on WordPress 3.5
wp-content/blogs.dir/7/ – This Multisite was created BEFORE 3.5
That’s all.
