Okay I have more news having spent most of the day trying to at least
figure out where this bug was introduced!

It appears to be introduced in linux kernel version 2.6.37:
 - Everything before this (version 2.6.36.4 and backwards) works on Ubuntu 
11.04, 10.10 and 10.04
 - Everything after this (version 2.6.37-rc1 and onwards, including 3.x) does 
not work on Ubuntu 10.10, 11.04, 11.10 and 12.04

As far as I can tell the same kernel module is responsible for this behaviour 
in all versions: ahci
Taken from lspci -v

Hope to have more information when I've found the relevant kernel changelog.
May also post the bug to the kernel bug tracker...

Cheers,
Richard

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https://bugs.launchpad.net/bugs/910999

Title:
  sil5744 over eSATA regression - repeated kernel failures & device
  initialisation times out

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