Thanks for your replies. It was so simple (and embarrassing) an error.
Jiaz is correct, it all started with a mistake in setting the permissions on the watchfolder. I use a permissions system based on a shared group because the server runs multiple services (torrent, usenet, web downloads) and I didn't want to create separate watchfolders and download targets for each user, plus there's the fact that I do web streaming so the unpacked files have to be accessed by a DLNA client or webserver as well.
The only reason I didn't notice is that it works for the other clients I use, but none of those create a directory in that path. This is all stored in a separate path on the SSD, the download progress and target directories are on a HDD and their permissions were correct from the beginning.
In case it can help anyone else with this or similar problems who finds the thread, I looked up my bash history and found the following commands that were executed as root. They create a directory that allows every user in the mediashare group to have read+write access to the directory but not access to create a directory.
mkdir watchfolder && chown -R :mediashare watchfolder && chmod -R 660 watchfolder && chmod g+s watchfolder && setfacl -d -m u::rw,g::rw,o::- watchfolder
After changing the chmod flag to 770 (and u::rwx,g::rwx,o::- to inherit file group ownership) the permissions are sufficient and it works fine. For some strange reason I had set it correctly for the download progress and target directories but not the watchfolder.
Thanks for the quick help