Very slow Firewire data transfer when connected to ext. HDD

Hi, I have both a Mini and a Mac book. When I connect my Macbook upto a WD MyBook Premium ext HDD and use SuperDuper! to back it up, I get an average copy speed of about 20 m/s. On my Mini I get about 2m/s!
Both the machines are more or less the latest version, that is less than 3 months old.
Any ideas why the Mini is sooooo slow?

Here are the ideas I can come up with ...
Be sure your Mini is configured to not run spotlight indexing on the external drive.
What model Mini do you have and how much RAM?
Are these incremental backups, or clones?
The last time I cloned my mini's hard drive with superduper over firewire, if I recall correctly I was getting speeds of about 10-12.
Another factor may be how full the source internal drives are: a Mac with a very full hard drive will be slower.
And I'm assuming you have multiple partitions on the external. The first partition probably has a slight speed advantage over the other partitions because of less head seeking movement.

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