hdparm seems to write the changes to the hdd firmware as Berion mentioned. The spindown business stopped when I reinstalled the hdd to my PS3.
As in the hdparm website guide you mentioned, I used
hdparm -i /dev/hda
hdb
hdc
hdd
and so on to identify the correct hdd.
Then when you are...
I just wanted to come and say that I fixed the same problem on my PS3 with the help of this program. Thanks guys!
I used the setting -S 24 which according to wikipedia article gives 120 seconds spindown time. It is still not 120 seconds, but over a minute is much better than the 4 seconds.