I've had this issue since 10.6 came out. I can't use rsync (3.0.6 for example) to clone a bootable installed 10.6. I have no problems cloning the installation media, just can't do an actual live bootable os.
If I ditto it, it's fine, and I can then use rsync to keep it up to date, but I have to remember to ditto on the first initial run.
Its been awhile since I experimented with it, but iirc it jus stalled during boot for no apparent reason, gear spinning and nothing useful in verbose.
