Linux NTFS to NTFS rsync repeatedly recopying files
As per my second update, the permissions of my user did not allow me to set times. Running the rsync using the root account on the destination machine, along with
--modify-window=5 gave me suitable behaviour. (If you don't have root access on the destination, the -u flag could help, but only if you're sure no-one will change the files on the remote system.)
Ideally you always want to use
robocopy as it handles variations in timestamps (upto 2 seconds for FAT). You can run in inside Wine but connecting to the remote host might be inconvenient.
edit: per Steve's comment, this feature appears to now be in rsync 3.0:
When comparing two timestamps, rsync treats the timestamps as being equal if they differ by no more than the modify-window value. This is normally 0 (for an exact match), but you may find it useful to set this to a larger value in some situations. In particular, when transferring to or from an MS Windows FAT filesystem (which represents times with a 2-second resolution), --modify-window=1 is useful (allowing times to differ by up to 1 second).