I have this too although maybe slightly different. I went to sync a directory with data on it (both the same for 99%) and lots of files aeound 30K. What it looks to me is that in 1.4.99 BTsync checks it's hash directly with the other file and can only do that 100x each 5 minutes. Why doesn't btsync just checks it's files on the new machine locally by the sync data between the two clients? For instance A has 3000 files B has 2990 of them. A sends it's filelist info(with the hashes to B ) B reads the hashes locally and checks them with it's own filelist. B marks the ones that are different and request those files from A. Now A just sends 100 hashes to B, B checks them and if all are good it waits 5 minutes till the next set comes.