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Are you running Tiger?
After 5 hours creating a clone of a disk running MacOS 10.4.8 (G4 iMac) to a new disk on my first use of Super Duper with Tiger, I noted it was running at around 2 MB/sec (had copied about 35 GB of 80 GB in the 5 hours) and the new disk in the firewire case was making a lot of noise (seagate 7200.10 320 Gb 16 MB cache PATA 7200 rpm). In my experience, SuperDuper (ver 80) has been quite fast under Panther (10.3.9).
So I decided to add the new disk to Spotlight's privacy tab (Super Duper left running) and the disk has become much quieter and the effective copy speed is increasing as I sit here and type this response (now 2.41 MB/sec and around another 10 GB has been copied in the half hour since implementing the change to spotlight). Therefore I am suspicious that Spotlight indexing was the cause of this slow behaviour.
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