I use rsync to keep my drives backed up under Windows 7 (using Cygwin). Windows permissions were getting messed up, but the solution was to disable ACL within Cygwin. I inserted this line into /etc/fstab.


none /cygdrive cygdrive binary,posix=0,user,noacl 0 0

There was no need to change the rsync command itself:


rsync -avn --stats <source> <destination>