I had this problem and the answer was found (a) in enabling ftp to write and (b) at least temporarily setting the directories to 777 although I think the latter permissions can be improved.
I run vsftp with chroot’d users. After finding no mention in apache logs, setting the permissions to 777, changing ftp group to www-data, enabling anonymous ftp to write, tearing my hair out, kicking the dog etc etc the penny eventually dropped that ftp was not allowed to write. I also upgraded a multi-site to 3.1.1 and that needs 777 set (well probably less) but returns the files 640.
It may be that a changed ftp configuration has tripped you up.