I use a freeware program called RipCord, which uses rsync, to back up my FileVaulted home on both my home and work laptops. Configured correctly, it works very well on 10.4 and also works fine on 10.5 once you exclude the .fseventsd directory (assuming the .fseventsd directory exists in the directory(s) you want to back up.) The .fseventsd directory is new and is the result of Time Machine. Time Machine relies on 10.5′s new FSEvent framework to track what files and folders have changed (and thus needs to be backed up) and the FSEvents framework relies on a single, constantly running daemon process called fseventsd that reads from /dev/fsevents and writes the events to log files on disk (stored in a .fseventsd directory at the root of the volume the events are for). So, 10.5 will create an invisible .fseventsd folder on the root level of your attached hard drive(s). If you’re using FileVault, an .fseventsd directory will also be created inside your FileVaulted home. Since the contents of that folder change frequently, rsync was having problems at the very beginning of my backup runs on 10.5 when I was trying to back up my FileVaulted home.
How I found this is that I’ve been having a number of RipCord errors on my home and work laptops when I’ve tried to run backups. Excluding that folder seems to have fixed the problem (I found out the reasons for it later), so on 10.5, add ~/.fseventsd to the list of excluded folders in RipCord.