For some reason, when running my rsync scripts, I kept getting output saying that files had been deleted when in fact they weren't. It looks like these were hidden files. Fortunately I found this site - http://wiki.ljackson.us/Rsync#Hidden_Files - and have slightly changed the syntax which now seems to work much better.
My revised scripts are:
rsync --progress /usr/bin/ssh -ave --stats --delete --exclude ".*" --exclude /iTunes\ Music/Downloads/Podcasts/ ~/Music/iTunes/"iTunes Music"/ /Volumes/1tb/"iTunes Music"
and
rsync --progress /usr/bin/ssh -ave --stats --delete --exclude ".*" --exclude /iPod\ Photo\ Cache/ --exclude /iPhoto\ Library --exclude /Photo\ Booth/ ~/Pictures/ /Volumes//Mac_backup/Pictures/