I ran wdidle3 /s300 (2x wdc drives, 2x samsung and a Seagate connected) and monitored that for a couple of days. It didn't seem to make a difference.
So, I ran wdidle3 /d on them (both drives connected still) 4 or 5 days ago, and my 2TB hard drive has gone nuts by the looks of the SMART data. Used wdidle3 /r to read it back and it said all was good. If I don't have any success, I'll have to dig my server out of the corner and disconnect all the sata drives and do them one at a time.
My WDC drives are just storage drives. No OS files are stored on them. I've just set them to spin down after 20 minutes with hdparm (I thought I'd done this already, but maybe not), so hopefully this will help things a little. The drives are only accessed while I'm watching or listening to something, and when a download completes and the resulting files are copied across (by scripts) to where they belong. 80% of the time they're idle, as I only use my HTPC for a couple of hours a day usually, even on weekends.
I've just tried a linux alternative to wdidle3 called idle3-tools (
http://sourceforge.net/projects/idle3-tools/) to set the timer back to 300 seconds. You can specify the device with that (/dev/sdb and sdc in my case), so hopefully that will make a difference.
I knew it was a bad sign when it took me 9 hours to successfully format the 2TB due to the 4k sectors and it lying to the OS about it. Should have bought another Samsung.