I had the same issue on my Gigabyte Z68AP-D3 mobo with the latest BIOS. I sent the following to Gigabyte:
I had to reinstall windows, and since I couldn't find the original CD for the motherboard, went to your website to download the drivers for the chipset, etc. I downloaded and installed the Intel RST version 11.6 you provided. After I had set up my SSD to be a cache disk, I rebooted, and it worked fine for a little. Then, after a few more reboots, Windows refused to start up, and just hung at the 'Starting Windows' screen. I did a little research and it seems like other people are having similar issue with the Z68 chipset and RST 11.6. After my third reinstall of Windows, I have now reverted back to version 10.6 of Intel RST and everything is working.