I believe this problem has to do with the differences in file systems across OSes. I too was having a similar issue, but ONLY when syncing with the OS X comp in the bunch. All of the other Windows PCs synced fine. As a test I stopped syncing with the Mac and instead ran a windows VM on it with BTSync installed, and there were no further sync issue as described in this thread. So the only solution I can then provide is to only use Windows. (Sorry I know it's not really constructive. I have no love for OS X, so being forced to bypass it was a good thing for me.) 2d