If it is an APM issue, then you could use QuietHDD to circumvent it.
Alternatively, you could use a HDDScan or CrystalDiskInfo command line to disable APM automatically at every bootup.
Hdparm may be a better alternative. You could launch it automatically from the Startup group from a BAT file. After hdparm does its thing, it then terminates and exits, leaving no impact on your resources.