Same problem here with:
Intel i7-2600, Gigabyte Z77-D3H, 16GB 1600MHz, SSD Mushkin Chronos MX 120GB, 2x WD10EZEX in RAID 0, WD10EARS. OS is Win 8.1 with all latest updates and drivers.
There is no "shutdown spin up" problem with 12.0.1.1019, but my RAID0 reading/writing performances are a lot worse then, according to HD Tune. (<200 MB/s vs ~300 MB/s with 12.9.0.1001)
Still, better that than "killing" HDDs at shutdown. 
I hope that Intel will solve this with the new version of the drivers.