Please post the operating systems involved, server version, if you are using symlinks on the server or btrfs etc.
(Debug) Log files of both server and clients would be helpful as well. See Having problems with UrBackup? Please read before posting for details.
Via looking if the files are listed in "C:\Program Files\UrBackup\urbackup\data\filelist.ub" you can also check if the problem is at the client or the server.