The option to ignore NTFS permissions has changed in Cygwin version 1.7. This might be what’s causing the problem.
Try adding the ‘noacl’ flag to your Cygwin mounts in C:\cygwin\etc\fstab, for example:
none /cygdrive cygdrive user,noacl,posix=0 0 0
You can pass custom permissions via rsync using the ‘chmod’ option:
rsync -rvz --chmod=ugo=rwX -e ssh source destination