One update. My system was overclocked when I saw this bug in Jaunty. It
was also overclocked when I ran Intrepid but I did not see any problems
with port multiplier.

Now with Jaunty if I disable overclocking and go to a regular speed it
works OK, no complains from system and port multiplier initializes
correctly. To me it looks like a timing issue.

-- 
Jaunty upgrade breaks SATA port multiplier
https://bugs.launchpad.net/bugs/383294
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