Comment 32 for bug 63937

I'm running 2.6.22-5 now, and there has been a development on this issue. Links to the LKML thread on the patch:

http://thread.gmane.org/gmane.linux.ide/18485

Basically, what it says is that it should now work as expected out of the box, if you write 0 to /sys/module/libata/parameters/spindown_compat before shutdown. This was done to support distros that were "fixed" in the mean time by doing the spindown in shutdown(8) or halt(8). Ubuntu is supposed to fix up halt(8) and shutdown(8), like it says on the accompanying web page:

http://linux-ata.org/shutdown.html

As for feisty, at this link there is a patch that toggles the default for stop_on_shutdown:

http://permalink.gmane.org/gmane.linux.hardware.thinkpad/29772

Unfortunately it apparently tries to spin down flash devices too, which leads to nasty but innocent error messages in the kernel output.