I've probably found the solution, but I need testers...

It seems that hdparm.conf isn't called anymore, because hdparm itself
isn't called during boot. So what you can do is forget about hdparm.conf
altogether, and alter the configuration file 20hdparm instead, which is
located in /etc/apm/event.d

So:
gksudo gedit /etc/apm/event.d/20hdparm

In the text, you'll see the following text block:
# The APMD_DRIVES setting specifies the drives to be changed.  Set
# this to an empty string to disable any changes.
#APMD_DRIVES=

Change the last line into 
APMD_DRIVES=/dev/sda

(assuming that your hard drive is sda, which is the most common
situation)

At the end of the next text block, you'll see this:
APMD_SPINDOWN=18

Change this into 254:
APMD_SPINDOWN=254

Then you'll see a text block starting with:
power_conserve ()

In that text block, you'll see this line:
"${HDPARM}" -q -S "${APMD_SPINDOWN}" "${DRIVE}" || true

Change the parameters for hdparm (delete -q -S and add -B instead):
"${HDPARM}" -B "${APMD_SPINDOWN}" "${DRIVE}" || true

Then you'll see a text block starting with:
power_performance ()

There, in the hdparm line, delete -q -S as well, and put instead -B. It becomes:
"${HDPARM}" -B 0 "${DRIVE}" || true

Save and close the configuration file. Then reboot your computer. All
should be well now. :-)

Note: change 254 into 0, if you want to disable spindown entirely.

As said, I need testers! Please help testing this workaround and post
your reactions here.

** Changed in: hdparm (Ubuntu)
       Status: Confirmed => Incomplete

-- 
[Lucid] hdparm.conf change doesn't have effect
https://bugs.launchpad.net/bugs/568120
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