Just out of curiosity, is there a chance your container has a few typos which may cause files to be deleted upon completion of transfer and seeding? It seemed odd that the items would vanish from the list when stopped, but, ignorantly, I never considered they were being deleted.
I log into my server to grab all the waiting files and the only thing left in the download folder is the one torrent that was still active. Only about 40GB of files missing.
Do you all have a beta testing program of some kind to help make sure this stuff doesn't happen? If so, sign me up because whoever is currently involved is not doing a very good job.