From the discussion Shirt Pocket Discussions - SuperDuper! and FileVault (a somewhat clearer explanation is in this discussion) it can be gathered that there are a few problems with SuperDuper! backups when using FileVault to encrypt your home directory: if the logged-in user is a FileVault user, their sparse image (the file where the actual home directory is located) is not backed up correctly and cannot be mounted correctly when booting from the backup.
The manufacturer suggests in the discussion to set up a second user who does not use FileVault and log out of the FileVault accounts to start a backup under this user.
Alternatively, you can of course create a separate backup for your home directory - the FileVault image is mounted normally when you are logged in. However, this means that the encryption is lost. This can of course be solved again with an encrypted SparseImage on a backup medium.
All in all, this is not the ultra-simple Mac user-compatible operation you would wish for. Precisely the home directory is the one that contains all the important things and whose contents you should back up regularly - but precisely this becomes cumbersome to back up as soon as FileVault is involved.
Of course, you can also do without FileVault - but somehow I don't want to entrust my private data on the notebook to an OpenFirmware startup password as the only security measure ...