Editing hdparm.conf alone is not enough and as I wrote in my previous comment, you have to run 'sudo update-rc.d hdparm defaults' too so that the hdparm init script is added to the approperiate runlevels (2, 3, 4 and 5). Runlevel 2 is the last runlevel and scripts in this runlevel are executed last, you can verify this by running the 'runlevel' command after you log in.
Editing hdparm.conf alone is not enough and as I wrote in my previous comment, you have to run 'sudo update-rc.d hdparm defaults' too so that the hdparm init script is added to the approperiate runlevels (2, 3, 4 and 5). Runlevel 2 is the last runlevel and scripts in this runlevel are executed last, you can verify this by running the 'runlevel' command after you log in.