I have the same problem. I use Windows x64 8.1 update 1, I have installed at first the version 13.1 and this was catastrophic!! I use 2 disk in RAID 0/1 on a Gigabyte X58 UD7 as storage drivers and an SSD 840 Evo on the Marvell SATA3 port as primary system disk.
My mechanical disks started to make horrible clicking noises every time I try to access a file or folder. I was really afraid to destroy them. So I uninstalled everything and installed the version 12.8. This was OK until discover the spin down - up - shutdown problem everyone here has. So I followed the suggestion to use the 11.7 or the windows supplied driver 12.0 and this has resolved the problem when I shutdown the pc.... BUT....
I still have this spinning problem when I suspend the PC!!
Could everyone else confirm that the problem still occurs with driver version 12.0 or 11.7 when you try to suspend the PC?
Could Intel tell us how to make our disks survive until you will release a fix (hopefully, also if I am not so optimist...)?
Many thanks!