I've also noticed similar things, like a bug where if I add a file to a zip, it will delete the destination file instead of updating it. For now, at least until the kinks are worked out, I am only going to use BT Sync to synchronize mostly static files. I don't think it's ready to synchronize directories that are in active use, bi-directionally. I find this perfectly acceptable as it is alpha release software and I'm not in a tizzy over it.
I would like to use Bit Torrent Sync to create shared storage pools used for multi-site synchronization of backup data. I would like to be able to write a management engine which queries BTSync to check on synch status at each remote storage pool and be presented in my own management interface so we can keep tabs on the status of backup transfer and, infact, whether new backup files were added to the storage pool. I would also like the BT Syncapp to run as a service such that it does not need to run in the user context. Thank you for your work on this, I am excited about what it can do for us!