The issue is a release critical bug, still open at the time of writing. However, there is a permanent fix available.
Obviously if you are installing Debian Stretch after this date, the bug may have been fixed, but here is the fix for anybody who needs it:
# systemctl --global enable obex
Arch Linux forum was where I found it- thanks go to them.
For me, file transfer does not work unless I have the Bluetooth settings dialogue window open.
