@RomanZ When I got my Syno I created a new admin and disabled the default user called 'admin'.
I installed the app with the new user and this always worked normally, until I installed DSM 6 last week. I reinstalled it, replaced the btsync file as you write in your manual but it doesn't started automatically.
I tried your /usr/local/bittorrentsync/bin/btsync --config /usr/local/bittorrentsync/var/sync.conf with that new admin and that starts the service, but after a reboot I have to do it again.
But I did what joeyvandijk writes, I login with my new admin, enabled the default admin, go to Package Center and just run the app (still logged in as as the new admin). And after that I disable the default admin again and it works like it should.