Files will not encrypt unless there is an active session to that folder from a user that has Encryption Desktop installed. This is the reason for the files not automatically encrypting.
I would recommend not using the "Force the encryption of files in the following folders" option. It will actually override the existing encryption access list from the folder, encrypting to the master keys of the first user to open an active session with that folder after the files are saved in that location.
If the FTP server is running Windows, you could possibly install SED on that system, so there could be an open session for that SED user when it transfers the files over.