[dnanian]

Well, the biggest problem with doing things like backups and safety clones when logged into a FileVault account is that your system is not in a decent 'state': Apple moves things around in funny ways to make FV work -- and when you restore it's in this 'logged in' state, but you're not logged in.

We definitely recommend logging out and into a non-FV account to backup and create safety clones. It's a lot cleaner that way. On top of that, people absolutely had issues with the Safety Clone and FileVault when /Users was shared -- we made the change because the volume wasn't mounting properly... I really don't know why yours is working, but you're welcome to make whatever changes you wish to the existing copy scripts, of course!