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.