You can't use SD! to back up a FileVault volume while you're logged into it (see the User's Guide) and expect to get a good backup in all cases.
I don't really have any solution for this "Restart" issue right now. We're unable to reproduce the problem here, but we're aware of the fact that people are having problems and we're trying to figure it out.
Please see
this post regarding 'trial copies' of SuperDuper.