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Ok, well the new backup is finished and I just booted up from it fine. It is also now showing exactly the same folders as the source.
Is it ok for me to assume that upgrading to Superduper 2.5 helped?
Dave, thank you very much for your time and advice. Although I now have Time Machine with Leopard I haven't considered using it because Super Duper seems to do exactly what I need; an emergency back up that I can boot from. A wonderful piece of software and worth every penny.
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