Same problem here. The commands no longer run after wake up so the drive status gets out of sync and as a result some drives never spin down. I am on 6.1.2 and it hasn't worked since a few versions ago but before that S3 Sleep worked perfectly other than the drive temps sometimes not showing but that's a different problem.
Try it with a reference to /usr/local/sbin/mdcmd
Thanks Bonienl. That seems to have fixed it.