That is done by the emhttp process which calls this script.
Sounds like something else is spinning the drives up.
I have a wrapper around the commands whilst in rc and was working on SAS spinup/down and fixes to smartctl.
Below is part of my go file and attached are the two wrappers.
hdparm and smartctl are moved and wrappers replace them and call the real command. You need to check it points to the correct real command in the wrapper.
it should only be the real command in the smartctl wrapper you need to correct as it was using smartctl.r5131 on my system if you want to use them.
mv /usr/sbin/smartctl /usr/sbin/smartctl.old
cp /boot/extras/smartctl.wrapper /usr/sbin/smartctl
chmod +x /usr/sbin/smartctl
cp /usr/sbin/hdparm /usr/local/sbin/hdparm.real
chmod +x /usr/local/sbin/hdparm.real
cp /boot/extras/hdparm.wrapper /usr/sbin/hdparm
chmod +x /usr/sbin/hdparm
You will get output in syslog so you can see what is using the commands and args.
Dec 20 13:47:39 Tower smartctl wrapper[17892]: caller is smartctl_type, grandpa is emhttpd, device /dev/sdb, args "-A /dev/sdb"
Dec 20 13:47:59 Tower hdparm wrapper[18010]: caller is bash, grandpa is ttyd, device /dev/sdb, args "-C /dev/sdb"
Wrapper and Smartctl.zip