I'm also running without the web ui (an unnecessary security risk IMO) and have thus answered "no" when asked by the installer to create a default config file. Instead I have custom config files in /etc/btsync. This seems to be working great, updating via apt-get stops and restarts my instances, all good. AFAIK my config files have the default options, but the shared folders are listed explicitly in the config files. Ok I wasn't aware of this, and I'm not sure I understand it. What is the correct behavior when I e.g. add new shared folders, or change a configuration option in my config files?