This isn't something we've tested, but in general terms you can't back up an image that you have open (e.g. FileVault). I don't know anything about Knox's "whole disk vault", but I don't think he allows encryption of the boot volume.
PGP does have a "whole disk encryption" option, and the next version of SuperDuper! (v2.6) will support it... and that should be bootable, too.
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--Dave Nanian
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