the best way I've found to sync Thunderbirds settings, even mail boxes across machines is by using TEBE
It's an off branch of FEBE (firefox) but since now Firefox has its own sync, FEBE became less, it's still great for Offline Backup purposes.
However FEBE is still the main tool I use to keep my Thunderbird settings across machines, since Thunderbird does not yet have a online sync tool built-in as Firefox does.
and TEBE has BOX.net sync option, so you can pick it up from another computer via TEBE by connecting to the same account, after each scheduled backup, or manual backup.
You can also specify what to backup and what to skip.