I'm using 3.3.10 on ubuntu 16.04.
Using webgui only - i have:
"Save files to location:" set to: /media/ExtHDD01/Downloads/
"Keep incomplete torrents in:" set to /media/ExtHDD01/Downloading/
Torrents download correctly to /media/ExtHDD01/Downloading/xxxxxxx/moviename
Torrents correctly get moved to /media/ExtHDD01/Downloads/ on complettion
Issue I have is /media/ExtHDD01/Downloading/ folder gets deleted, rather than /media/ExtHDD01/Downloading/xxxxxxxx as expected