I think I owe the fix I used.

As mentioned before, I first tried the hdparm'ing things, but then, I found the default setting can be changed by specific HDD manufacturer tools. I like it better, since It means a reinstall won't require to fix it again - and also I don't believe it is an OS issue.

See here for original idea :
http://ubuntuforums.org/showpost.php?p=368...mp;postcount=22

And here for hitashi feature tool, that allows changing apm parameters directly on the hard drive :
http://www.hitachigst.com/hdd/support/download.htm