I'm starting to get a feel for what might be the problem here. The problem only ever seems to occur when I make a change to files on my laptop, which btsync will want to sync, but then very shortly afterwards shut off or suspend the laptop. It's as if btsync creates a list of files that were updated, files it thinks it now has the newest version of, in preparation to update other computers. The update occurs, the other machines download the files, but before btsync can confirm that everything is synchronized completely, it gets cut off by the shutdown or suspend. Then, next time the laptop is powered on, that list still exists, and btsync attempts to continue by broadcasting the files as new updates again. Files which are now out of date. Ideally, btsync shouldn't persist that list (assuming that's what is actually happening). On startup it should scrap any activities it was in the middle of and start fresh. But barring that, I've had some success by waiting a few minutes between the last file change I make and when I shut off the laptop. I also moved btsync startup so it is launched by a system service, rather than launched by X, so that during shutdown it isn't abruptly killed by X closing, giving it a bit more time to clean up.